Running as unit: rb-build-amd64_35-78648.service; invocation ID: be12967d782f4af5bea36de3997d8fd2 ==================================================================================== Thu Sep 18 22:09:13 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_35) on jenkins, called using "infom01-amd64 infom02-amd64" as arguments. Thu Sep 18 22:09:13 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-3bhnVcBr" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 22:09:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Thu Sep 18 22:09:13 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Acmvdx' Thu Sep 18 22:09:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Thu Sep 18 22:09:13 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-8tD0BF' ok, let's check if promod3 is building anywhere yet… ok, promod3 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of promod3 in unstable on amd64 on jenkins now. 1st build will be done on infom01-amd64.debian.net. 2nd build will be done on infom02-amd64.debian.net. ============================================================================= Thu Sep 18 22:09:22 UTC 2025 I: starting to build promod3/unstable/amd64 on jenkins on '2025-09-18 22:09' Thu Sep 18 22:09:22 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_35/78648/console.log 1758233362 amd64 unstable promod3 Thu Sep 18 22:09:22 UTC 2025 I: Downloading source for unstable/promod3=3.4.2+ds-1 --2025-09-18 22:09:22-- http://deb.debian.org/debian/pool/main/p/promod3/promod3_3.4.2%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3240 (3.2K) [text/prs.lines.tag] Saving to: ‘promod3_3.4.2+ds-1.dsc’ 0K ... 100% 394M=0s 2025-09-18 22:09:22 (394 MB/s) - ‘promod3_3.4.2+ds-1.dsc’ saved [3240/3240] --2025-09-18 22:09:22-- http://deb.debian.org/debian/pool/main/p/promod3/promod3_3.4.2%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3240 (3.2K) [text/prs.lines.tag] Saving to: ‘promod3_3.4.2+ds-1.dsc’ 0K ... 100% 394M=0s 2025-09-18 22:09:22 (394 MB/s) - ‘promod3_3.4.2+ds-1.dsc’ saved [3240/3240] Thu Sep 18 22:09:22 UTC 2025 I: promod3_3.4.2+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: promod3 Binary: libpromod3-core-dev, libpromod3-core3.4, libpromod3-loop-dev, libpromod3-loop3.4, libpromod3-modelling-dev, libpromod3-modelling3.4, libpromod3-scoring-dev, libpromod3-scoring3.4, libpromod3-sidechain-dev, libpromod3-sidechain3.4, promod3, promod3-data, python3-promod3 Architecture: any all Version: 3.4.2+ds-1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://openstructure.org/promod3/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/debichem-team/promod3 Vcs-Git: https://salsa.debian.org/debichem-team/promod3.git Build-Depends: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost Package-List: libpromod3-core-dev deb libdevel optional arch=any libpromod3-core3.4 deb libs optional arch=any libpromod3-loop-dev deb libdevel optional arch=any libpromod3-loop3.4 deb libs optional arch=any libpromod3-modelling-dev deb libdevel optional arch=any libpromod3-modelling3.4 deb libs optional arch=any libpromod3-scoring-dev deb libdevel optional arch=any libpromod3-scoring3.4 deb libs optional arch=any libpromod3-sidechain-dev deb libdevel optional arch=any libpromod3-sidechain3.4 deb libs optional arch=any promod3 deb science optional arch=all promod3-data deb science optional arch=all python3-promod3 deb python optional arch=any Checksums-Sha1: fe26d94587be71b7fb6ccc240ad859fac92c81fb 398726492 promod3_3.4.2+ds.orig.tar.xz 957992a7723d0725c56268d9d25b608b36644180 5884 promod3_3.4.2+ds-1.debian.tar.xz Checksums-Sha256: 7a46576b3c73bceaba25b36b10be9b3fc5ef4bdbc1a957d01c7c68eae76dc1b1 398726492 promod3_3.4.2+ds.orig.tar.xz eeee3ec35d048e7fd7cbe8022cf25289d40772ecd89f197a6e30b7182523191f 5884 promod3_3.4.2+ds-1.debian.tar.xz Files: 47857c7c2a40f7ac9798956b6a601c3d 398726492 promod3_3.4.2+ds.orig.tar.xz bbcb4746ab7c2a9e997d04feff944be5 5884 promod3_3.4.2+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmfrtxASHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHuWMP/iOF/ZMsDErNcI3c3OOYXeiFFQMcAE/W gJ1H40Qk9nUeRf6scL6mn4TREKJ5a6DOT1jyuJvgl4P4q1398OA5zIay6Qv68dS/ f4JLO+eu0I/zzn34bPh1LKDwjLDkSeMqBFzBz+f7VIfBjXgj84Dxxk+5ZcC26QsS iFrqFX1fb6y9+/eDalk8bdZLlsUvU/FCP/gUMZeGlPO77gcnY7ACrqeLC45pTAJ5 tQyejwrs/Ogl6KWtxmNa/QVIDqGWQIJxiFjkVT6zszNRC25q4n3nOxitl4AgtQ0T ccLzaB1WH01xwcg2aDs1bqXsm9ebX8oxgi4N+7ccprEQtC2eOuwt9xBBRHi32jvu SjPJdgJHkmnSzWmb3Av9KG2/74w85qVrrV/pTM4CXT6CSrtxI5IlXpIIYMfy8ypC CUOsuiRRPerkhkK9Bskd+pmDIJG/+ewNXnCqxjVBksjdPPOwhg35EFfCvfWQ0YMB TbVw4SZcvJzwvsLrUcooWetZv4OKj+ak2nfAFWCJqAGGPdSpRPfbVPlYI8gvqBF0 vESGB+4C6dzoivJnrmWzqKtQhAiunzmDLwZwHh/clKCVQHwCYRAYhRfK/LIP6ry5 UW4qNx08eCFWi38qIAhytI18z90lpDAM7a6T/gsskcu15ZM/MA8q7ZbMNOs+eV36 OH3gi8YDkZlR =2u1I -----END PGP SIGNATURE----- Thu Sep 18 22:09:22 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 22:09:22 UTC 2025 I: Starting 1st build on remote node infom01-amd64.debian.net. Thu Sep 18 22:09:22 UTC 2025 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Thu Sep 18 22:09:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Thu Sep 18 22:09:22 UTC 2025 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-YA1l5G' ==================================================================================== Thu Sep 18 22:09:23 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "1 promod3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw 3.4.2+ds-1" as arguments. Thu Sep 18 22:09:23 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-VNbYMZuq" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 22:09:23 UTC 2025 I: Downloading source for unstable/promod3=3.4.2+ds-1 Reading package lists... NOTICE: 'promod3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/promod3.git Please use: git clone https://salsa.debian.org/debichem-team/promod3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 399 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (dsc) [3240 B] Get:2 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (tar) [399 MB] Get:3 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (diff) [5884 B] Fetched 399 MB in 7s (58.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'promod3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/promod3.git Please use: git clone https://salsa.debian.org/debichem-team/promod3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 399 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (dsc) [3240 B] Get:2 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (tar) [399 MB] Get:3 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (diff) [5884 B] Fetched 399 MB in 7s (58.1 MB/s) Download complete and in download only mode ============================================================================= Building promod3 in unstable on amd64 on infom01-amd64 now. Date: Thu Sep 18 22:09:30 UTC 2025 Date UTC: Thu Sep 18 22:09:30 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 10:09:30 -12 2025 I: pbuilder-time-stamp: 1758233370 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [promod3_3.4.2+ds-1.dsc] I: copying [./promod3_3.4.2+ds.orig.tar.xz] I: copying [./promod3_3.4.2+ds-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./promod3_3.4.2+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.4.2+ds dpkg-source: info: unpacking promod3_3.4.2+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.4.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-OST.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/886740/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6b7da0c95e804347af6604500b044982' 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='886740' 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.yYuuEnzw/pbuilderrc_cE7q --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1 --logfile b1/build.log promod3_3.4.2+ds-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/886740/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: amd64 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: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 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 libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-test-dev; however: Package libboost-test-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-base-dev; however: Package libost-base-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-conop-dev; however: Package libost-conop-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-geom-dev; however: Package libost-geom-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-img-dev; however: Package libost-img-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-info-dev; however: Package libost-info-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-io-dev; however: Package libost-io-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-alg-dev; however: Package libost-mol-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-dev; however: Package libost-mol-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-mm-dev; however: Package libost-mol-mm-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-alg-dev; however: Package libost-seq-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-dev; however: Package libost-seq-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on openstructure (>= 2.5.0); however: Package openstructure is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-ost; however: Package python3-ost 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas3{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcups2t64{a} libcurl4t64{a} libdav1d7{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgbm1{a} libgcc-14-dev{a} libgcrypt20{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglu1-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu76{a} libidn2-0{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libnghttp2-14{a} libnghttp3-9{a} libopengl0{a} libopenjp2-7{a} libopenmm8.1{a} libost-base-dev{a} libost-base2.9{a} libost-bindings2.9{a} libost-conop-dev{a} libost-conop2.9{a} libost-db2.9{a} libost-geom-dev{a} libost-geom2.9{a} libost-gfx2.9{a} libost-gui2.9{a} libost-img-alg2.9{a} libost-img-dev{a} libost-img2.9{a} libost-info-dev{a} libost-info2.9{a} libost-io-dev{a} libost-io2.9{a} libost-mol-alg-dev{a} libost-mol-alg2.9{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.9{a} libost-mol2.9{a} libost-seq-alg-dev{a} libost-seq-alg2.9{a} libost-seq-dev{a} libost-seq2.9{a} libp11-kit0{a} libparasail8{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5printsupport5t64{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5widgets5t64{a} libqt5xml5t64{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libstdc++-14-dev{a} libsvtav1enc2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{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} libxdmcp6{a} libxext6{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2-16{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} libzopfli1{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} netbase{a} openstructure{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-attr{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-fs{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-ost{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-platformdirs{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-sympy{a} python3-tk{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xkb-data{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common krb5-locales libarchive-cpio-perl libcifpp-data libglib2.0-data libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pooch python3-yaml qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 307 newly installed, 0 to remove and 0 not upgraded. Need to get 356 MB of archives. After unpacking 1327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 91 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-2 [190 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-5 [336 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-5 [352 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-5 [265 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-5 [385 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-5 [313 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-5 [337 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-5 [488 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-5 [560 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.1-1 [41.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.125-2 [64.1 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-6 [25.9 MB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.2.3-1 [10.3 MB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.2.3-1 [46.0 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.24.0-2+b1 [28.5 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 25.2.3-1 [123 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.4+dfsg-1 [32.4 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.321.0-1 [133 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.2.3-1 [47.6 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.2.3-1 [116 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-7 [14.6 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.5.0-1 [517 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.16.1-1 [112 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.16.1-1 [26.8 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.28.1-1 [26.3 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.7-1 [22.6 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.28.1-1 [143 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libost-base2.9 amd64 2.9.3-2 [34.9 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libost-base-dev amd64 2.9.3-2 [29.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libost-geom2.9 amd64 2.9.3-2 [66.4 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libost-mol2.9 amd64 2.9.3-2 [395 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.17+dfsg-3 [2017 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.17+dfsg-3 [136 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libost-info2.9 amd64 2.9.3-2 [168 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libost-seq2.9 amd64 2.9.3-2 [91.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libost-bindings2.9 amd64 2.9.3-2 [204 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libost-conop2.9 amd64 2.9.3-2 [190 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libost-conop-dev amd64 2.9.3-2 [23.5 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libost-db2.9 amd64 2.9.3-2 [45.6 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libost-geom-dev amd64 2.9.3-2 [30.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libost-img2.9 amd64 2.9.3-2 [144 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libost-img-alg2.9 amd64 2.9.3-2 [170 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libost-gfx2.9 amd64 2.9.3-2 [433 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg2.9 amd64 2.9.3-2 [370 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libost-io2.9 amd64 2.9.3-2 [884 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libparasail8 amd64 2.6.2+dfsg-2 [1890 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg2.9 amd64 2.9.3-2 [255 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.17+dfsg-3 [235 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.17+dfsg-3 [756 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.1-1 [23.5 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [16.7 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.10-1 [18.4 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2.1 [113 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2.1 [16.2 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.17+dfsg-3 [3767 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.17+dfsg-3 [2591 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libost-gui2.9 amd64 2.9.3-2 [507 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libost-img-dev amd64 2.9.3-2 [44.6 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libost-info-dev amd64 2.9.3-2 [21.9 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libost-io-dev amd64 2.9.3-2 [53.5 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg-dev amd64 2.9.3-2 [32.6 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libost-mol-dev amd64 2.9.3-2 [59.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm2.9 amd64 2.9.3-2 [299 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm-dev amd64 2.9.3-2 [29.8 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg-dev amd64 2.9.3-2 [179 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libost-seq-dev amd64 2.9.3-2 [26.0 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.17-3 [2760 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.17+dfsg-3 [135 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.17-3 [150 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.17+dfsg-3 [220 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.17+dfsg-3 [161 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-8 [1172 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 16.0.0+ds-1 [324 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.17.0-1+b1 [61.6 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-2+b2 [2801 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.9.3-2 [3990 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.9.3-2 [93.1 MB] Fetched 356 MB in 7s (52.1 MB/s) Preconfiguring packages ... 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Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) 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Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libqhull-r8.0:amd64 (2020.2-7) ... Setting up libxcb-render-util0:amd64 (0.3.10-1) ... Setting up xkb-data (2.42-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libxcb-icccm4:amd64 (0.4.2-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-5) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libpcre2-16-0:amd64 (10.46-1) ... 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Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb-xinerama0:amd64 (1.17.0-2+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libsqlite3-dev:amd64 (3.46.1-8) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-4) ... Setting up libavahi-common-data:amd64 (0.8-17) ... Setting up libdbus-1-3:amd64 (1.16.2-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.50-1) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Setting up libtcl8.6:amd64 (8.6.17+dfsg-1) ... Setting up autopoint (0.23.1-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libgav1-1:amd64 (0.19.0-3+b1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libsensors5:amd64 (1:3.6.2-2) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up libboost-test1.83.0:amd64 (1.83.0-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up libvulkan1:amd64 (1.4.321.0-1) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up libwebp7:amd64 (1.5.0-0.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up libdav1d7:amd64 (1.5.1-1) ... Setting up libmtdev1t64:amd64 (1.1.7-1) ... 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Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up libstdc++-14-dev:amd64 (14.3.0-8) ... Setting up libdrm-common (2.4.125-2) ... Setting up libyuv0:amd64 (0.0.1916.20250814-1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up libevdev2:amd64 (1.13.4+dfsg-1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libost-geom2.9:amd64 (2.9.3-2) ... Setting up libwacom-common (2.16.1-1) ... Setting up libxkbcommon0:amd64 (1.7.0-2.1) ... Setting up libwayland-client0:amd64 (1.24.0-2+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19 (1:19.1.7-6) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up libavif16:amd64 (1.3.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libboost1.83-dev:amd64 (1.83.0-5) ... Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libboost-program-options1.83-dev:amd64 (1.83.0-5) ... Setting up libavahi-common3:amd64 (0.8-17) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libboost-test-dev:amd64 (1.83.0.2+b2) ... Setting up dh-autoreconf (21) ... Setting up libglib2.0-0t64:amd64 (2.84.4-3) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libost-mol2.9 (2.9.3-2) ... Setting up shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxkbcommon-x11-0:amd64 (1.7.0-2.1) ... Setting up libeigen3-dev (3.4.0-5) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-5) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up groff-base (1.23.0-9) ... Setting up libharfbuzz0b:amd64 (11.5.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-5) ... Setting up libost-geom-dev (2.9.3-2) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libicu-dev:amd64 (76.1-4) ... Setting up libavahi-client3:amd64 (0.8-17) ... Setting up libost-conop2.9 (2.9.3-2) ... Setting up libgudev-1.0-0:amd64 (238-7) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.7-1) ... Setting up libwacom9:amd64 (2.16.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up libdrm-intel1:amd64 (2.4.125-2) ... Setting up libost-mol-dev (2.9.3-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-5) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.13-tk (3.13.7-1) ... Setting up python3-platformdirs (4.4.0-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up libinput-bin (1.28.1-1) ... Setting up libost-conop-dev (2.9.3-2) ... Setting up python3-fs (2.4.16-8) ... Setting up libqt5core5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:amd64 (0.10.3-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-cycler (0.12.1-2) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-5) ... Setting up python3-numpy (1:2.2.4+ds-1.2) ... Setting up python3-pyqt5.sip (12.17.0-1+b1) ... Setting up python3-lxml:amd64 (6.0.1-1) ... Setting up libqt5sql5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up libcups2t64:amd64 (2.4.10-4) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up dh-python (6.20250414) ... Setting up libinput10:amd64 (1.28.1-1) ... Setting up python3-sympy (1.14.0-2) ... Setting up python3-attr (25.3.0-1) ... Setting up mesa-libgallium:amd64 (25.2.3-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up libqt5dbus5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-scipy (1.15.3-1.1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up libcurl4t64:amd64 (8.16.0-1) ... Setting up libgbm1:amd64 (25.2.3-1) ... Setting up python3-lz4 (4.4.4+dfsg-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-5) ... 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Setting up python3-pyqt5 (5.15.11+dfsg-2+b2) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-5) ... Setting up python3-ost (2.9.3-2) ... Setting up openstructure (2.9.3-2) ... Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && 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 > ../promod3_3.4.2+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.2+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_configure -- \ -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib .. -- The CXX compiler identification is GNU 15.2.0 -- The C compiler identification is GNU 15.2.0 -- 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 CMake Warning (dev) at CMakeLists.txt:58 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- 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 CMake Warning (dev) at cmake_support/PROMOD3.cmake:980 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:997 (get_compiler_version) CMakeLists.txt:87 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.13.7", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed CMake Warning (dev) at cmake_support/PROMOD3.cmake:1029 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost package: python313 CMake Warning (dev) at cmake_support/PROMOD3.cmake:1043 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: unit_test_framework CMake Warning (dev) at cmake_support/PROMOD3.cmake:1050 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: filesystem system CMake Warning (dev) at cmake_support/PROMOD3.cmake:1054 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: iostreams CMake Warning (dev) at cmake_support/PROMOD3.cmake:1057 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: program_options CMake Warning (dev) at cmake_support/PROMOD3.cmake:1060 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: regex -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): config/src/CMakeLists.txt:8 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:593 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/init/CMakeLists.txt:9 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) sidechain/tests/CMakeLists.txt:11 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:464 (copy_if_different) scripts/CMakeLists.txt:12 (script) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scripts/CMakeLists.txt:15 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:6 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:7 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:8 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:9 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. -- ProMod3 will be built with the following options: OpenStructure (-DOST_ROOT) : /usr Compound library (-DCOMPOUND_LIB): /var/cache/openstructure/compounds.chemlib Optimized (-DOPTIMIZE) : ON Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 -- Configuring done (2.7s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data [ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header [ 1%] Built target loop_data_dir cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend [ 1%] Built target sidechain_data_dir make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" [ 1%] Built target scoring_pymod [ 1%] Built target sidechain_pymod [ 1%] Built target loop_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py [ 1%] Built target scoring_data_dir make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target subst_pm make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend [ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake [ 1%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend [ 1%] Built target create_stage make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build [ 1%] Built target bash-completion make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh [ 1%] Built target core_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target init_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py [ 1%] Built target promod3_scripts [ 1%] Built target actions cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh [ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh [ 1%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh [ 1%] Built target promod3_modelling_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_sidechain_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_scoring_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_core.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.4 -o ../../stage/lib64/libpromod3_core.so.3.4.2 CMakeFiles/promod3_core.dir/cluster.cc.o CMakeFiles/promod3_core.dir/geom_base.cc.o CMakeFiles/promod3_core.dir/geom_stems.cc.o CMakeFiles/promod3_core.dir/superpose.cc.o CMakeFiles/promod3_core.dir/graph.cc.o CMakeFiles/promod3_core.dir/tree.cc.o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_core.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4 ../../stage/lib64/libpromod3_core.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_core make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_runtime_profiling.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/backbone.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_geom.cc [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/wrap_core.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/amino_acid_atoms.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_env.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/bb_trace_param.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/density_creator.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_positions.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/fragger.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_constructor.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_rule_lookup.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -MF CMakeFiles/promod3_loop.dir/idx_handler.cc.o.d -o CMakeFiles/promod3_loop.dir/idx_handler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/idx_handler.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -MF CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o.d -o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -MF CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/mm_system_creator.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/psipred_prediction.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -MF CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o.d -o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/torsion_sampler.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_rule_lookup.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:22, from /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, 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++/15/bits/basic_string.h:991:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:1165:19: 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] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /usr/include/boost/variant.hpp:17, from /usr/include/ost/generic_property.hh:34, from /usr/include/ost/mol/entity_base.hh:25, from /usr/include/ost/mol/entity_view.hh:27, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:29: /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/15/string:44: In static member function 'static 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++/15/bits/basic_string.h:451:23, 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++/15/bits/basic_string.h:969:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/char_traits.h:352:16: 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] 352 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 19%] Linking CXX shared library ../../stage/lib64/libpromod3_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_loop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_loop.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_loop.so.3.4 -o ../../stage/lib64/libpromod3_loop.so.3.4.2 CMakeFiles/promod3_loop.dir/all_atom_env.cc.o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o CMakeFiles/promod3_loop.dir/backbone.cc.o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o CMakeFiles/promod3_loop.dir/density_creator.cc.o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o CMakeFiles/promod3_loop.dir/frag_db.cc.o CMakeFiles/promod3_loop.dir/fragger.cc.o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/idx_handler.cc.o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o CMakeFiles/promod3_loop.dir/structure_db.cc.o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4 ../../stage/lib64/libpromod3_loop.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target promod3_loop make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o [ 21%] Building CXX object 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loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_positions.cc [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o [ 22%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/bb_dep_rotamer_lib.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o [ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_forcefield_lookup.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/disulfid.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_score_base.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc [ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_loop_object_loader.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/particle_scoring.cc [ 28%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_overall_scorer.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_particle_scoring.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_particle_scoring.cc [ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_particle_scoring.cc [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cb_packing_score.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_cruncher.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_density.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_group.cc [ 33%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_id.cc [ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_score.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_env_listener.cc [ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/density_score.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_entry.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:17: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = bool]', inlined from 'boost::python::extract::operator result_type() const [with T = bool]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: /usr/include/boost/python/extract.hpp:185:11: warning: '*(bool*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: note: '' declared here 66 | v.push_back(boost::python::extract(l[i])); | ^~~~~~~~~~~~~~~~ [ 40%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc [ 42%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc [ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc [ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_rotamer_constructor.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc [ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_rotamer_constructor.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/constraint_constructor.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_overall_scorer.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_rotamer_constructor.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/subrotamer_optimizer.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc [ 52%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_packing_score.cc /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_loop.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 52%] Built target _loop [ 53%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_clash_score.cc [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_scoring.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_scoring.so.3.4 -o ../../stage/lib64/libpromod3_scoring.so.3.4.2 CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o CMakeFiles/promod3_scoring.dir/clash_score.cc.o CMakeFiles/promod3_scoring.dir/density_score.cc.o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4 ../../stage/lib64/libpromod3_scoring.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 53%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_scwrl3_energy_functions.cc [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_density_scorer.cc [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -MF CMakeFiles/_scoring.dir/export_object_loader.cc.o.d -o CMakeFiles/_scoring.dir/export_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_object_loader.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_pairwise_functions.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_constraint_constructor.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/wrap_scoring.cc [ 60%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_sidechain.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.2 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4 ../../stage/lib64/libpromod3_sidechain.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 60%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 60%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_connector.cc [ 60%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_frame.cc [ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_disulfid.cc [ 63%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/extension_scheme.cc [ 63%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -MF CMakeFiles/promod3_modelling.dir/gap.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_graph.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o [ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap_extender.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_cruncher.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_density.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/all_atom_relaxer.cc [ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_ids.cc [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/ccd.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_lib.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_sidechain_object_loader.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/loop_candidate.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_constructor.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_subrotamer_optimizer.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc [ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/wrap_sidechain.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_cooler.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/rigid_blocks.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_reconstructor.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_env_listener.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_scoring.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so CMakeFiles/_scoring.dir/export_backbone_score.cc.o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o CMakeFiles/_scoring.dir/export_object_loader.cc.o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o CMakeFiles/_scoring.dir/export_density_scorer.cc.o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _scoring In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc:17: /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 4 of type 'const double*' 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 = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o CMakeFiles/_sidechain.dir/export_particle.cc.o CMakeFiles/_sidechain.dir/export_rotamer.cc.o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_modelling.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_modelling.so.3.4 -o ../../stage/lib64/libpromod3_modelling.so.3.4.2 CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o CMakeFiles/promod3_modelling.dir/gap.cc.o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o CMakeFiles/promod3_modelling.dir/model.cc.o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o CMakeFiles/promod3_modelling.dir/ccd.cc.o CMakeFiles/promod3_modelling.dir/kic.cc.o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o CMakeFiles/promod3_modelling.dir/score_container.cc.o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o CMakeFiles/promod3_modelling.dir/afdb.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_modelling.so.3.4 ../../stage/lib64/libpromod3_modelling.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK 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&& /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -MF CMakeFiles/_modelling.dir/export_model.cc.o.d -o CMakeFiles/_modelling.dir/export_model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_model.cc cd 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-I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -MF CMakeFiles/_modelling.dir/export_motif_finder.cc.o.d -o CMakeFiles/_modelling.dir/export_motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_motif_finder.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_rigid_blocks.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_sidechain_reconstructor.cc [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_afdb.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:21: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: note: '' declared here 112 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: note: '' declared here 179 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: note: '' declared here 47 | String seq = extract(args[0]); | ^ [ 90%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_modelling.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so CMakeFiles/_modelling.dir/export_extension_scheme.cc.o CMakeFiles/_modelling.dir/export_gap.cc.o CMakeFiles/_modelling.dir/export_gap_extender.cc.o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o CMakeFiles/_modelling.dir/export_loop_closure.cc.o CMakeFiles/_modelling.dir/export_model.cc.o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o CMakeFiles/_modelling.dir/export_score_container.cc.o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o CMakeFiles/_modelling.dir/export_motif_finder.cc.o CMakeFiles/_modelling.dir/export_afdb.cc.o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_modelling.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data 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loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data 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cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data 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scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat [ 98%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 97%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat [ 98%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [ 94%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target generate_scoring_data_cbeta_scorer.dat [ 98%] Built target generate_scoring_data_cb_packing_scorer.dat [ 98%] Built target generate_scoring_data_hbond_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" [ 98%] Built target generate_loop_data_ff_lookup_charmm.dat [ 98%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_ss_agreement_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat [100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_helical.dat [100%] Built target generate_loop_data_torsion_sampler_extended.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_coil.dat [100%] Built target generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 check ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target actions make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq_ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target test_data_actions make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] running checks test_actions.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_actions.py" Compound library not available. Some functionality may not work as expected. . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_actions.py_run make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests//test_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/broken_on_purpose.chemlib /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.json /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/alignment.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_1.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_2trg.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_3.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_nel.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_sw.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_data_core make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target promod3_core_headers make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src 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/build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 4%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_check_io.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_portable_binary.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_graph_minimizer.cc [ 6%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/tests.cc [ 6%] Linking CXX executable ../../tests/core/test_suite_core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_core.dir/link.d CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target test_suite_core make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target core_pymod make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/pymod/CMakeFiles/_core.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 8%] Built target _core make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] running checks for module core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/test_suite_core Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] Built target test_suite_core_run make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] running checks test_setcompoundschemlib.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_setcompoundschemlib.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.094s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] Built target test_setcompoundschemlib.py_run make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_helper.py" Compound library not available. Some functionality may not work as expected. ............ ---------------------------------------------------------------------- Ran 12 tests in 0.001s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_helper.py_run make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_pm3argparse.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_pm3argparse.py" Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- Ran 66 tests in 1.198s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_pm3argparse.py_run make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target loop_data_dir make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target modelling_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target promod3_loop_headers make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/src/CMakeFiles/promod3_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target promod3_loop make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target loop_pymod make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/pymod/CMakeFiles/_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target _loop make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target promod3_scoring_headers make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target scoring_pymod make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/pymod/CMakeFiles/_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target _scoring make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target promod3_sidechain_headers make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/src/CMakeFiles/promod3_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target sidechain_pymod make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/pymod/CMakeFiles/_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target _sidechain make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target promod3_modelling_headers make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/src/CMakeFiles/promod3_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 67%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/pymod/CMakeFiles/_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 73%] Built target _modelling make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init_pymod make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_ff_lookup_charmm.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler_coil.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_extended.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_helical.dat make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_frag_db.dat make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target loop_data make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A_with_gap.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_ref.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/CHARMM27.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target test_data_loop make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -MF CMakeFiles/test_suite_loop.dir/test_backbone.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_backbone.cc [ 79%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -MF CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_forcefield.cc [ 79%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -MF CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_hydrogens.cc [ 80%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -MF CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_mm_system_creator.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_psipred_prediction.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_sidechain_construction.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_torsion_sampler.cc [ 82%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -MF CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_structuredb.cc [ 82%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o -MF CMakeFiles/test_suite_loop.dir/tests.cc.o.d -o CMakeFiles/test_suite_loop.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/tests.cc [ 84%] Linking CXX executable ../../tests/loop/test_suite_loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_loop.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_loop.dir/link.d CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o CMakeFiles/test_suite_loop.dir/tests.cc.o -o ../../tests/loop/test_suite_loop -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] running checks for module loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/test_suite_loop Running 68 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop_run make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target scoring_data_dir make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_aa_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_cb_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 86%] Built target generate_scoring_data_cbeta_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_reduced_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_hbond_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_ss_agreement_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_torsion_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target scoring_data make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/1CRNA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/clash_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target test_data_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_score_base.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_scorer.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc:73:33: warning: 'promod3::loop::AllAtomPositions scoring::{anonymous}::GenerateTestPos(const String&, uint, uint)' defined but not used [-Wunused-function] 73 | promod3::loop::AllAtomPositions GenerateTestPos( | ^~~~~~~~~~~~~~~ [ 89%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/tests.cc [ 89%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_scoring.dir/link.d CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o CMakeFiles/test_suite_scoring.dir/tests.cc.o -o ../../tests/scoring/test_suite_scoring -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 89%] Built target test_suite_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] running checks for module scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/test_suite_scoring Running 20 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target test_suite_scoring_run make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target sidechain_data_dir make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target generate_sidechain_data_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target sidechain_data make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/data/all_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_data_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_frame_construction.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_rotamers.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o -MF CMakeFiles/test_suite_sidechain.dir/tests.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/tests.cc [ 93%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_sidechain.dir/link.d CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -o ../../tests/sidechain/test_suite_sidechain -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] running checks for module sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/test_suite_sidechain Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain_run make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_build.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_final.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRNA.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1mcg.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2dbs.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/del.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ff_NAD.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_almost_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_shifted_nter.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/hetero-punched.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E 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/usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/port_str_db.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/smtl2bl4.1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ter.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/double_gap_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_data_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_candidates.cc [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_closing.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstructor.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o -MF CMakeFiles/test_suite_modelling.dir/tests.cc.o.d -o CMakeFiles/test_suite_modelling.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/tests.cc [ 95%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_modelling.dir/link.d CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 95%] Built target test_suite_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks for module modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/test_suite_modelling Running 7 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_suite_modelling_run make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_close_gaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_close_gaps.py" Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- Ran 33 tests in 18.121s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_close_gaps.py_run make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_gap_extension.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_gap_extension.py" Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- Ran 6 tests in 0.013s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_gap_extension.py_run make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_modelling.py" Compound library not available. Some functionality may not work as expected. ..............Alignment-structure mismatch at pos 0 in chain A, alignment is 'X' structure residue is 'S'. Ok for modified residue SEP. ...residue A.GLY8 has conflicting atom CA - skipping atom. residue A.GLY8 is missing atoms CA ........ ---------------------------------------------------------------------- Ran 25 tests in 0.068s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_modelling.py_run make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_pipeline.py" Compound library not available. Some functionality may not work as expected. Switched to slower reference platform of OpenMM! ............... ---------------------------------------------------------------------- Ran 15 tests in 28.434s OK OpenMM CPU platform not available. Skipping almost_on_top check. phenix.molprobity is missing. Please install it and make it available in your PATH to execute test testMolProbity. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_pipeline.py_run make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_ring_punches.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.078s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_ring_punches.py_run make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_sidechain_reconstruction.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstruction.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 1.618s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_sidechain_reconstruction.py_run make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_alignment_fiddling.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.009s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_alignment_fiddling.py_run make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target subst_pm make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target promod3_scripts make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-model.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 4.016s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-model.py_run make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-rawmodel.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-rawmodel.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 1.059s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-rawmodel.py_run make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] running checks test_action_help.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_help.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.025s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target test_action_help.py_run make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target codetest make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./check_io.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./cluster.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./dynamic_spatial_organizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./export_helper.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_stems.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./message.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_sink.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_source.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_serializer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./runtime_profiling.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./superpose.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./enumerator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tree.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tetrahedral_polytope.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph_minimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./eigen_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/pm3argparse.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_env.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_positions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./amino_acid_atoms.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./backbone.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./bb_trace_param.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./data_bag.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_hash_table.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Up-to-date: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./density_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./forcefield_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./frag_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./fragger.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./idx_handler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./loop_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./mm_system_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./psipred_prediction.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./stem_geom.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./torsion_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./ushort_vec.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db_custom_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scoring_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cb_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./density_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./torsion_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_scoring_function.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./constraint_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scwrl3_energy_functions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./disulfid.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./frame.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_cruncher.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_density.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_group.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_id.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_entry.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_reader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_connector.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./subrotamer_optimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./extension_scheme.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap_extender.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./model.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./all_atom_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./backbone_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./ccd.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./kic.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./loop_candidate.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_closer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_cooler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./rigid_blocks.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./score_container.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./scoring_weights.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_reconstructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./motif_finder.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./robin_hood.h -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./afdb.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_denovo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_planar_rings.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/bin/pm -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install for PKG in core loop modelling scoring sidechain; do \ dh_install -p libpromod3-${PKG}-dev usr/include/promod3/${PKG}; \ dh_install -p libpromod3-${PKG}-dev usr/lib64/libpromod3_${PKG}.so usr/lib/x86_64-linux-gnu; \ dh_install -p libpromod3-${PKG}3.4 usr/lib64/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib64 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:421: renaming _modelling.so to _modelling.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _loop.so to _loop.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package promod3: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.2+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.4.2+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.4.2+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/886740 and its subdirectories I: Current time: Thu Sep 18 10:25:00 -12 2025 I: pbuilder-time-stamp: 1758234300 Thu Sep 18 22:25:00 UTC 2025 I: Signing ./b1/promod3_3.4.2+ds-1_amd64.buildinfo as promod3_3.4.2+ds-1_amd64.buildinfo.asc Thu Sep 18 22:25:00 UTC 2025 I: Signed ./b1/promod3_3.4.2+ds-1_amd64.buildinfo as ./b1/promod3_3.4.2+ds-1_amd64.buildinfo.asc Thu Sep 18 22:25:00 UTC 2025 - build #1 for promod3/unstable/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 22:25:00 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-VNbYMZuq, removing. /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw: total 20 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 22:25 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 22:09 b2 -rw-rw-r-- 1 jenkins jenkins 3240 Apr 1 10:00 promod3_3.4.2+ds-1.dsc -rw------- 1 jenkins jenkins 4359 Sep 18 22:09 rbuildlog.tdEmpvo /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1: total 802828 -rw-r--r-- 1 jenkins jenkins 943605 Sep 18 22:25 build.log -rw-r--r-- 1 jenkins jenkins 24480 Sep 18 22:25 libpromod3-core-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2656392 Sep 18 22:25 libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 95292 Sep 18 22:25 libpromod3-core3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 35500 Sep 18 22:25 libpromod3-loop-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5353248 Sep 18 22:25 libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 290316 Sep 18 22:25 libpromod3-loop3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 37152 Sep 18 22:25 libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12137636 Sep 18 22:25 libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 307252 Sep 18 22:25 libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 18072 Sep 18 22:25 libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4526828 Sep 18 22:25 libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 181792 Sep 18 22:25 libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19428 Sep 18 22:25 libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4495028 Sep 18 22:25 libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 238772 Sep 18 22:25 libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 371418628 Sep 18 22:25 promod3-data_3.4.2+ds-1_all.deb -rw-r--r-- 1 jenkins jenkins 5884 Sep 18 22:25 promod3_3.4.2+ds-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3240 Sep 18 22:25 promod3_3.4.2+ds-1.dsc -rw-r--r-- 1 jenkins jenkins 11036 Sep 18 22:25 promod3_3.4.2+ds-1_all.deb -rw-r--r-- 1 jenkins jenkins 18989 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 19871 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 7769 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1470 Sep 18 22:25 promod3_3.4.2+ds-1_source.changes -rw-r--r-- 1 jenkins jenkins 398726492 Sep 18 22:25 promod3_3.4.2+ds.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 19269372 Sep 18 22:25 python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1060036 Sep 18 22:25 python3-promod3_3.4.2+ds-1_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2: total 0 Thu Sep 18 22:25:07 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 10:09:30 -12 2025 I: pbuilder-time-stamp: 1758233370 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [promod3_3.4.2+ds-1.dsc] I: copying [./promod3_3.4.2+ds.orig.tar.xz] I: copying [./promod3_3.4.2+ds-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./promod3_3.4.2+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.4.2+ds dpkg-source: info: unpacking promod3_3.4.2+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.4.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-OST.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/886740/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6b7da0c95e804347af6604500b044982' 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='886740' 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.yYuuEnzw/pbuilderrc_cE7q --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1 --logfile b1/build.log promod3_3.4.2+ds-1.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/886740/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: amd64 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: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 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 libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-test-dev; however: Package libboost-test-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-base-dev; however: Package libost-base-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-conop-dev; however: Package libost-conop-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-geom-dev; however: Package libost-geom-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-img-dev; however: Package libost-img-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-info-dev; however: Package libost-info-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-io-dev; however: Package libost-io-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-alg-dev; however: Package libost-mol-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-dev; however: Package libost-mol-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-mm-dev; however: Package libost-mol-mm-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-alg-dev; however: Package libost-seq-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-dev; however: Package libost-seq-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on openstructure (>= 2.5.0); however: Package openstructure is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-ost; however: Package python3-ost 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas3{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcups2t64{a} libcurl4t64{a} libdav1d7{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgbm1{a} libgcc-14-dev{a} libgcrypt20{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglu1-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu76{a} libidn2-0{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libnghttp2-14{a} libnghttp3-9{a} libopengl0{a} libopenjp2-7{a} libopenmm8.1{a} libost-base-dev{a} libost-base2.9{a} libost-bindings2.9{a} libost-conop-dev{a} libost-conop2.9{a} libost-db2.9{a} libost-geom-dev{a} libost-geom2.9{a} libost-gfx2.9{a} libost-gui2.9{a} libost-img-alg2.9{a} libost-img-dev{a} libost-img2.9{a} libost-info-dev{a} libost-info2.9{a} libost-io-dev{a} libost-io2.9{a} libost-mol-alg-dev{a} libost-mol-alg2.9{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.9{a} libost-mol2.9{a} libost-seq-alg-dev{a} libost-seq-alg2.9{a} libost-seq-dev{a} libost-seq2.9{a} libp11-kit0{a} libparasail8{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5printsupport5t64{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5widgets5t64{a} libqt5xml5t64{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libstdc++-14-dev{a} libsvtav1enc2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{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} libxdmcp6{a} libxext6{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2-16{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} libzopfli1{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} netbase{a} openstructure{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-attr{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-fs{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-ost{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-platformdirs{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-sympy{a} python3-tk{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xkb-data{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common krb5-locales libarchive-cpio-perl libcifpp-data libglib2.0-data libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pooch python3-yaml qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 307 newly installed, 0 to remove and 0 not upgraded. Need to get 356 MB of archives. After unpacking 1327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 91 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-2 [190 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-5 [336 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-5 [352 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-5 [265 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-5 [385 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-5 [313 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-5 [337 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-5 [488 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-5 [560 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.1-1 [41.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.125-2 [64.1 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-6 [25.9 MB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.2.3-1 [10.3 MB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.2.3-1 [46.0 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.24.0-2+b1 [28.5 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 25.2.3-1 [123 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.4+dfsg-1 [32.4 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.321.0-1 [133 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.2.3-1 [47.6 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.2.3-1 [116 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-7 [14.6 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.5.0-1 [517 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.16.1-1 [112 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.16.1-1 [26.8 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.28.1-1 [26.3 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.7-1 [22.6 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.28.1-1 [143 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libost-base2.9 amd64 2.9.3-2 [34.9 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libost-base-dev amd64 2.9.3-2 [29.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libost-geom2.9 amd64 2.9.3-2 [66.4 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libost-mol2.9 amd64 2.9.3-2 [395 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.17+dfsg-3 [2017 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.17+dfsg-3 [136 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libost-info2.9 amd64 2.9.3-2 [168 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libost-seq2.9 amd64 2.9.3-2 [91.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libost-bindings2.9 amd64 2.9.3-2 [204 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libost-conop2.9 amd64 2.9.3-2 [190 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libost-conop-dev amd64 2.9.3-2 [23.5 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libost-db2.9 amd64 2.9.3-2 [45.6 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libost-geom-dev amd64 2.9.3-2 [30.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libost-img2.9 amd64 2.9.3-2 [144 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libost-img-alg2.9 amd64 2.9.3-2 [170 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libost-gfx2.9 amd64 2.9.3-2 [433 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg2.9 amd64 2.9.3-2 [370 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libost-io2.9 amd64 2.9.3-2 [884 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libparasail8 amd64 2.6.2+dfsg-2 [1890 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg2.9 amd64 2.9.3-2 [255 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.17+dfsg-3 [235 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.17+dfsg-3 [756 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.1-1 [23.5 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [16.7 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.10-1 [18.4 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2.1 [113 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2.1 [16.2 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.17+dfsg-3 [3767 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.17+dfsg-3 [2591 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libost-gui2.9 amd64 2.9.3-2 [507 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libost-img-dev amd64 2.9.3-2 [44.6 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libost-info-dev amd64 2.9.3-2 [21.9 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libost-io-dev amd64 2.9.3-2 [53.5 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg-dev amd64 2.9.3-2 [32.6 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libost-mol-dev amd64 2.9.3-2 [59.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm2.9 amd64 2.9.3-2 [299 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm-dev amd64 2.9.3-2 [29.8 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg-dev amd64 2.9.3-2 [179 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libost-seq-dev amd64 2.9.3-2 [26.0 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.17-3 [2760 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.17+dfsg-3 [135 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.17-3 [150 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.17+dfsg-3 [220 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.17+dfsg-3 [161 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-8 [1172 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 16.0.0+ds-1 [324 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.17.0-1+b1 [61.6 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-2+b2 [2801 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.9.3-2 [3990 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.9.3-2 [93.1 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && 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 > ../promod3_3.4.2+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.2+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_configure -- \ -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib .. -- The CXX compiler identification is GNU 15.2.0 -- The C compiler identification is GNU 15.2.0 -- 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 CMake Warning (dev) at CMakeLists.txt:58 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- 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 CMake Warning (dev) at cmake_support/PROMOD3.cmake:980 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:997 (get_compiler_version) CMakeLists.txt:87 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.13.7", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed CMake Warning (dev) at cmake_support/PROMOD3.cmake:1029 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost package: python313 CMake Warning (dev) at cmake_support/PROMOD3.cmake:1043 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: unit_test_framework CMake Warning (dev) at cmake_support/PROMOD3.cmake:1050 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: filesystem system CMake Warning (dev) at cmake_support/PROMOD3.cmake:1054 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: iostreams CMake Warning (dev) at cmake_support/PROMOD3.cmake:1057 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: program_options CMake Warning (dev) at cmake_support/PROMOD3.cmake:1060 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: regex -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): config/src/CMakeLists.txt:8 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:593 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/init/CMakeLists.txt:9 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) sidechain/tests/CMakeLists.txt:11 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:464 (copy_if_different) scripts/CMakeLists.txt:12 (script) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scripts/CMakeLists.txt:15 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:6 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:7 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:8 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:9 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. -- ProMod3 will be built with the following options: OpenStructure (-DOST_ROOT) : /usr Compound library (-DCOMPOUND_LIB): /var/cache/openstructure/compounds.chemlib Optimized (-DOPTIMIZE) : ON Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 -- Configuring done (2.7s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[3]: Entering directory 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make -f 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'/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data [ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header [ 1%] Built target loop_data_dir cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend [ 1%] Built target sidechain_data_dir make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" [ 1%] Built target scoring_pymod [ 1%] Built target sidechain_pymod [ 1%] Built target loop_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py [ 1%] Built target scoring_data_dir make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target subst_pm make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend [ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake [ 1%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend [ 1%] Built target create_stage make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build [ 1%] Built target bash-completion make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh [ 1%] Built target core_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target init_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py [ 1%] Built target promod3_scripts [ 1%] Built target actions cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh [ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh [ 1%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh [ 1%] Built target promod3_modelling_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_sidechain_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_scoring_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_core.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.4 -o ../../stage/lib64/libpromod3_core.so.3.4.2 CMakeFiles/promod3_core.dir/cluster.cc.o CMakeFiles/promod3_core.dir/geom_base.cc.o CMakeFiles/promod3_core.dir/geom_stems.cc.o CMakeFiles/promod3_core.dir/superpose.cc.o CMakeFiles/promod3_core.dir/graph.cc.o CMakeFiles/promod3_core.dir/tree.cc.o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_core.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4 ../../stage/lib64/libpromod3_core.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_core make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_runtime_profiling.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/backbone.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_geom.cc [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/wrap_core.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/amino_acid_atoms.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_env.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/bb_trace_param.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/density_creator.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF 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loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/fragger.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_rule_lookup.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -MF CMakeFiles/promod3_loop.dir/idx_handler.cc.o.d -o CMakeFiles/promod3_loop.dir/idx_handler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/idx_handler.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -MF CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o.d -o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -MF CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/mm_system_creator.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/psipred_prediction.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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/build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:22, from /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, 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++/15/bits/basic_string.h:991:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:1165:19: 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] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /usr/include/boost/variant.hpp:17, from /usr/include/ost/generic_property.hh:34, from /usr/include/ost/mol/entity_base.hh:25, from /usr/include/ost/mol/entity_view.hh:27, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:29: /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/15/string:44: In static member function 'static 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++/15/bits/basic_string.h:451:23, 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++/15/bits/basic_string.h:969:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/char_traits.h:352:16: 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] 352 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 19%] Linking CXX shared library ../../stage/lib64/libpromod3_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_loop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_loop.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_loop.so.3.4 -o ../../stage/lib64/libpromod3_loop.so.3.4.2 CMakeFiles/promod3_loop.dir/all_atom_env.cc.o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o CMakeFiles/promod3_loop.dir/backbone.cc.o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o CMakeFiles/promod3_loop.dir/density_creator.cc.o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o CMakeFiles/promod3_loop.dir/frag_db.cc.o CMakeFiles/promod3_loop.dir/fragger.cc.o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/idx_handler.cc.o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o CMakeFiles/promod3_loop.dir/structure_db.cc.o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4 ../../stage/lib64/libpromod3_loop.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target promod3_loop make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o [ 21%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_amino_acid_atoms.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_positions.cc [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o [ 22%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/bb_dep_rotamer_lib.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o [ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_forcefield_lookup.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/disulfid.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_score_base.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_fragger.cc [ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc [ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_loop_object_loader.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/particle_scoring.cc [ 28%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_overall_scorer.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_particle_scoring.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_particle_scoring.cc [ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_particle_scoring.cc [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cb_packing_score.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_cruncher.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_density.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_group.cc [ 33%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_id.cc [ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_score.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/density_score.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_entry.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:17: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = bool]', inlined from 'boost::python::extract::operator result_type() const [with T = bool]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: /usr/include/boost/python/extract.hpp:185:11: warning: '*(bool*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: note: '' declared here 66 | v.push_back(boost::python::extract(l[i])); | ^~~~~~~~~~~~~~~~ [ 40%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc [ 42%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc [ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc [ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_rotamer_constructor.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc [ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_overall_scorer.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_rotamer_constructor.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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/build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc [ 52%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_packing_score.cc /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_loop.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 52%] Built target _loop [ 53%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c 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CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o CMakeFiles/promod3_scoring.dir/clash_score.cc.o CMakeFiles/promod3_scoring.dir/density_score.cc.o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4 ../../stage/lib64/libpromod3_scoring.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 53%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_scwrl3_energy_functions.cc [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_density_scorer.cc [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -MF CMakeFiles/_scoring.dir/export_object_loader.cc.o.d -o CMakeFiles/_scoring.dir/export_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_object_loader.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_pairwise_functions.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_constraint_constructor.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/wrap_scoring.cc [ 60%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_sidechain.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.2 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4 ../../stage/lib64/libpromod3_sidechain.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 60%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 60%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_connector.cc [ 60%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_frame.cc [ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_disulfid.cc [ 63%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/extension_scheme.cc [ 63%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -MF CMakeFiles/promod3_modelling.dir/gap.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_graph.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o [ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap_extender.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_cruncher.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_density.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/all_atom_relaxer.cc [ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_ids.cc [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/ccd.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_lib.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_sidechain_object_loader.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/loop_candidate.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_constructor.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_subrotamer_optimizer.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc [ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/wrap_sidechain.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_cooler.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/rigid_blocks.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_reconstructor.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_env_listener.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_scoring.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so CMakeFiles/_scoring.dir/export_backbone_score.cc.o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o CMakeFiles/_scoring.dir/export_object_loader.cc.o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o CMakeFiles/_scoring.dir/export_density_scorer.cc.o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _scoring In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc:17: /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 4 of type 'const double*' 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 = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o CMakeFiles/_sidechain.dir/export_particle.cc.o CMakeFiles/_sidechain.dir/export_rotamer.cc.o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_modelling.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_modelling.so.3.4 -o ../../stage/lib64/libpromod3_modelling.so.3.4.2 CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o CMakeFiles/promod3_modelling.dir/gap.cc.o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o CMakeFiles/promod3_modelling.dir/model.cc.o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o CMakeFiles/promod3_modelling.dir/ccd.cc.o CMakeFiles/promod3_modelling.dir/kic.cc.o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o CMakeFiles/promod3_modelling.dir/score_container.cc.o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o CMakeFiles/promod3_modelling.dir/afdb.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_modelling.so.3.4 ../../stage/lib64/libpromod3_modelling.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK 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&& /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -MF CMakeFiles/_modelling.dir/export_model.cc.o.d -o CMakeFiles/_modelling.dir/export_model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_model.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -MF CMakeFiles/_modelling.dir/export_monte_carlo.cc.o.d -o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -MF CMakeFiles/_modelling.dir/export_scoring_weights.cc.o.d -o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -MF CMakeFiles/_modelling.dir/export_motif_finder.cc.o.d -o CMakeFiles/_modelling.dir/export_motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_motif_finder.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_rigid_blocks.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_sidechain_reconstructor.cc [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_afdb.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:21: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: note: '' declared here 112 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: note: '' declared here 179 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: note: '' declared here 47 | String seq = extract(args[0]); | ^ [ 90%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_modelling.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so CMakeFiles/_modelling.dir/export_extension_scheme.cc.o CMakeFiles/_modelling.dir/export_gap.cc.o CMakeFiles/_modelling.dir/export_gap_extender.cc.o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o CMakeFiles/_modelling.dir/export_loop_closure.cc.o CMakeFiles/_modelling.dir/export_model.cc.o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o CMakeFiles/_modelling.dir/export_score_container.cc.o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o CMakeFiles/_modelling.dir/export_motif_finder.cc.o CMakeFiles/_modelling.dir/export_afdb.cc.o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_modelling.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat [ 98%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 97%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat [ 98%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [ 94%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target generate_scoring_data_cbeta_scorer.dat [ 98%] Built target generate_scoring_data_cb_packing_scorer.dat [ 98%] Built target generate_scoring_data_hbond_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" [ 98%] Built target generate_loop_data_ff_lookup_charmm.dat [ 98%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_ss_agreement_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat [100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_helical.dat [100%] Built target generate_loop_data_torsion_sampler_extended.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_coil.dat [100%] Built target generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 check ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target actions make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq_ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target test_data_actions make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] running checks test_actions.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_actions.py" Compound library not available. Some functionality may not work as expected. . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_actions.py_run make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests//test_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/broken_on_purpose.chemlib /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.json /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/alignment.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_1.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_2trg.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_3.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_nel.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_sw.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_data_core make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target promod3_core_headers make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src 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/build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 4%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_check_io.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_portable_binary.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_graph_minimizer.cc [ 6%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/tests.cc [ 6%] Linking CXX executable ../../tests/core/test_suite_core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_core.dir/link.d CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target test_suite_core make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target core_pymod make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/pymod/CMakeFiles/_core.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 8%] Built target _core make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] running checks for module core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/test_suite_core Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] Built target test_suite_core_run make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] running checks test_setcompoundschemlib.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_setcompoundschemlib.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.094s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] Built target test_setcompoundschemlib.py_run make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_helper.py" Compound library not available. Some functionality may not work as expected. ............ ---------------------------------------------------------------------- Ran 12 tests in 0.001s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_helper.py_run make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_pm3argparse.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_pm3argparse.py" Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- Ran 66 tests in 1.198s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_pm3argparse.py_run make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target loop_data_dir make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target modelling_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target promod3_loop_headers make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/src/CMakeFiles/promod3_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target promod3_loop make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target loop_pymod make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/pymod/CMakeFiles/_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target _loop make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target promod3_scoring_headers make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target scoring_pymod make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/pymod/CMakeFiles/_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target _scoring make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target promod3_sidechain_headers make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/src/CMakeFiles/promod3_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target sidechain_pymod make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/pymod/CMakeFiles/_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target _sidechain make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target promod3_modelling_headers make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/src/CMakeFiles/promod3_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 67%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/pymod/CMakeFiles/_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 73%] Built target _modelling make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init_pymod make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_ff_lookup_charmm.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler_coil.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_extended.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_helical.dat make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_frag_db.dat make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target loop_data make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A_with_gap.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1akyA.horiz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_ref.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/CHARMM27.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target test_data_loop make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_all_atom_env.cc [ 78%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_all_atom_positions.cc [ 78%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -MF CMakeFiles/test_suite_loop.dir/test_backbone.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_backbone.cc [ 79%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -MF CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_forcefield.cc [ 79%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -MF CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_hydrogens.cc [ 80%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_idx_handler.cc [ 80%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -MF CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_mm_system_creator.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_psipred_prediction.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_sidechain_construction.cc [ 81%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_torsion_sampler.cc [ 82%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -MF CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/test_structuredb.cc [ 82%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o -MF CMakeFiles/test_suite_loop.dir/tests.cc.o.d -o CMakeFiles/test_suite_loop.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/tests/tests.cc [ 84%] Linking CXX executable ../../tests/loop/test_suite_loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_loop.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_loop.dir/link.d CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o CMakeFiles/test_suite_loop.dir/tests.cc.o -o ../../tests/loop/test_suite_loop -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] running checks for module loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/test_suite_loop Running 68 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop_run make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target scoring_data_dir make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_aa_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_cb_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 86%] Built target generate_scoring_data_cbeta_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_reduced_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_hbond_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_ss_agreement_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_torsion_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target scoring_data make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/1CRNA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/clash_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target test_data_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_score_base.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_scorer.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc:73:33: warning: 'promod3::loop::AllAtomPositions scoring::{anonymous}::GenerateTestPos(const String&, uint, uint)' defined but not used [-Wunused-function] 73 | promod3::loop::AllAtomPositions GenerateTestPos( | ^~~~~~~~~~~~~~~ [ 89%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/tests.cc [ 89%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_scoring.dir/link.d CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o CMakeFiles/test_suite_scoring.dir/tests.cc.o -o ../../tests/scoring/test_suite_scoring -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 89%] Built target test_suite_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] running checks for module scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/test_suite_scoring Running 20 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target test_suite_scoring_run make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target sidechain_data_dir make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target sidechain_data make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/data/all_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_data_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_frame_construction.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_rotamers.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o -MF CMakeFiles/test_suite_sidechain.dir/tests.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/tests.cc [ 93%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_sidechain.dir/link.d CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -o ../../tests/sidechain/test_suite_sidechain -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] running checks for module sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/test_suite_sidechain Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain_run make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_build.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_final.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRNA.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1mcg.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2dbs.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/del.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ff_NAD.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_almost_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_shifted_nter.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/hetero-punched.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/neighbor-punched.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/port_frag_db.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/port_str_db.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/smtl2bl4.1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ter.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/double_gap_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_data_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_candidates.cc [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_closing.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstructor.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o -MF CMakeFiles/test_suite_modelling.dir/tests.cc.o.d -o CMakeFiles/test_suite_modelling.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/tests.cc [ 95%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_modelling.dir/link.d CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 95%] Built target test_suite_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks for module modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/test_suite_modelling Running 7 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_suite_modelling_run make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_close_gaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_close_gaps.py" Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- Ran 33 tests in 18.121s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_close_gaps.py_run make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_gap_extension.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_gap_extension.py" Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- Ran 6 tests in 0.013s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_gap_extension.py_run make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_modelling.py" Compound library not available. Some functionality may not work as expected. ..............Alignment-structure mismatch at pos 0 in chain A, alignment is 'X' structure residue is 'S'. Ok for modified residue SEP. ...residue A.GLY8 has conflicting atom CA - skipping atom. residue A.GLY8 is missing atoms CA ........ ---------------------------------------------------------------------- Ran 25 tests in 0.068s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_modelling.py_run make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_pipeline.py" Compound library not available. Some functionality may not work as expected. Switched to slower reference platform of OpenMM! ............... ---------------------------------------------------------------------- Ran 15 tests in 28.434s OK OpenMM CPU platform not available. Skipping almost_on_top check. phenix.molprobity is missing. Please install it and make it available in your PATH to execute test testMolProbity. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_pipeline.py_run make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_ring_punches.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.078s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_ring_punches.py_run make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_sidechain_reconstruction.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstruction.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 1.618s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_sidechain_reconstruction.py_run make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_alignment_fiddling.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.009s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_alignment_fiddling.py_run make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target subst_pm make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target promod3_scripts make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-model.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 4.016s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-model.py_run make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-rawmodel.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-rawmodel.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 1.059s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-rawmodel.py_run make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] running checks test_action_help.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_help.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.025s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target test_action_help.py_run make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target codetest make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./check_io.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./cluster.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./dynamic_spatial_organizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./export_helper.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_stems.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./message.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_sink.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_source.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_serializer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./runtime_profiling.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./superpose.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./enumerator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tree.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tetrahedral_polytope.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph_minimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./eigen_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/pm3argparse.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_env.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_positions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./amino_acid_atoms.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./backbone.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./bb_trace_param.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./data_bag.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_hash_table.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Up-to-date: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./density_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./forcefield_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./frag_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./fragger.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./idx_handler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./loop_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./mm_system_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./psipred_prediction.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./stem_geom.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./torsion_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./ushort_vec.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db_custom_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scoring_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cb_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./density_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./torsion_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_scoring_function.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./constraint_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scwrl3_energy_functions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./disulfid.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./frame.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_cruncher.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_density.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_group.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_id.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_entry.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_reader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_connector.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./subrotamer_optimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./extension_scheme.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap_extender.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./model.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./all_atom_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./backbone_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./ccd.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./kic.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./loop_candidate.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_closer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_cooler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./rigid_blocks.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./score_container.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./scoring_weights.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_reconstructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./motif_finder.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./robin_hood.h -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./afdb.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_denovo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_planar_rings.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/bin/pm -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install for PKG in core loop modelling scoring sidechain; do \ dh_install -p libpromod3-${PKG}-dev usr/include/promod3/${PKG}; \ dh_install -p libpromod3-${PKG}-dev usr/lib64/libpromod3_${PKG}.so usr/lib/x86_64-linux-gnu; \ dh_install -p libpromod3-${PKG}3.4 usr/lib64/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib64 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:421: renaming _modelling.so to _modelling.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _loop.so to _loop.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package promod3: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.2+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.4.2+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.4.2+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/886740 and its subdirectories I: Current time: Thu Sep 18 10:25:00 -12 2025 I: pbuilder-time-stamp: 1758234300 Thu Sep 18 22:25:08 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Thu Sep 18 22:25:08 UTC 2025 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Thu Sep 18 22:25:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Thu Sep 18 22:25:08 UTC 2025 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UXH51z' ==================================================================================== Thu Oct 22 04:48:09 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "2 promod3 unstable /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw 3.4.2+ds-1" as arguments. Thu Oct 22 04:48:09 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-8PY1Urxr" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Oct 22 04:48:09 UTC 2026 I: Downloading source for unstable/promod3=3.4.2+ds-1 Reading package lists... NOTICE: 'promod3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/promod3.git Please use: git clone https://salsa.debian.org/debichem-team/promod3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 399 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (dsc) [3240 B] Get:2 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (tar) [399 MB] Get:3 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (diff) [5884 B] Fetched 399 MB in 4s (90.2 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'promod3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/promod3.git Please use: git clone https://salsa.debian.org/debichem-team/promod3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 399 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (dsc) [3240 B] Get:2 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (tar) [399 MB] Get:3 http://deb.debian.org/debian unstable/main promod3 3.4.2+ds-1 (diff) [5884 B] Fetched 399 MB in 4s (90.2 MB/s) Download complete and in download only mode ============================================================================= Re-Building promod3 in unstable on amd64 on infom02-amd64 now. Date: Thu Oct 22 04:48:13 UTC 2026 Date UTC: Thu Oct 22 04:48:13 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/pbuilderrc_C3hE + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' promod3 = debian-installer -o promod3 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' promod3 = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/pbuilderrc_C3hE --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2 --logfile b2/build.log promod3_3.4.2+ds-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 22 18:48:14 +14 2026 I: pbuilder-time-stamp: 1792644494 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [promod3_3.4.2+ds-1.dsc] I: copying [./promod3_3.4.2+ds.orig.tar.xz] I: copying [./promod3_3.4.2+ds-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./promod3_3.4.2+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.4.2+ds dpkg-source: info: unpacking promod3_3.4.2+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.4.2+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find-OST.patch dpkg-source: info: applying add-python3-shebangs.patch dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 22 04:48 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=08d8bffcef3645ec981dc6890b8ba4c5 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3517703 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/pbuilderrc_C3hE --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2 --logfile b2/build.log promod3_3.4.2+ds-1.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3517703/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: amd64 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: cmake, debhelper-compat (= 13), dh-python, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libboost-python-dev, libboost-test-dev, libeigen3-dev, libost-base-dev, libost-conop-dev, libost-geom-dev, libost-img-dev, libost-info-dev, libost-io-dev, libost-mol-alg-dev, libost-mol-dev, libost-mol-mm-dev, libost-seq-alg-dev, libost-seq-dev, libsqlite3-dev, openstructure (>= 2.5.0), python3-dev, python3-ost dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 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 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 libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-python-dev; however: Package libboost-python-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-test-dev; however: Package libboost-test-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-base-dev; however: Package libost-base-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-conop-dev; however: Package libost-conop-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-geom-dev; however: Package libost-geom-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-img-dev; however: Package libost-img-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-info-dev; however: Package libost-info-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-io-dev; however: Package libost-io-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-alg-dev; however: Package libost-mol-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-dev; however: Package libost-mol-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-mol-mm-dev; however: Package libost-mol-mm-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-alg-dev; however: Package libost-seq-alg-dev is not installed. pbuilder-satisfydepends-dummy depends on libost-seq-dev; however: Package libost-seq-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on openstructure (>= 2.5.0); however: Package openstructure is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-ost; however: Package python3-ost 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libabsl20240722{a} libaom3{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavif16{a} libblas3{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-python-dev{a} libboost-python1.83-dev{a} libboost-python1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-test-dev{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost-thread1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcups2t64{a} libcurl4t64{a} libdav1d7{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm2{a} libedit2{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgav1-1{a} libgbm1{a} libgcc-14-dev{a} libgcrypt20{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglib2.0-0t64{a} libglu1-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu76{a} libidn2-0{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig0{a} libjpeg62-turbo{a} libjs-sphinxdoc{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libldap2{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libnghttp2-14{a} libnghttp3-9{a} libopengl0{a} libopenjp2-7{a} libopenmm8.1{a} libost-base-dev{a} libost-base2.9{a} libost-bindings2.9{a} libost-conop-dev{a} libost-conop2.9{a} libost-db2.9{a} libost-geom-dev{a} libost-geom2.9{a} libost-gfx2.9{a} libost-gui2.9{a} libost-img-alg2.9{a} libost-img-dev{a} libost-img2.9{a} libost-info-dev{a} libost-info2.9{a} libost-io-dev{a} libost-io2.9{a} libost-mol-alg-dev{a} libost-mol-alg2.9{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.9{a} libost-mol2.9{a} libost-seq-alg-dev{a} libost-seq-alg2.9{a} libost-seq-dev{a} libost-seq2.9{a} libp11-kit0{a} libparasail8{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5printsupport5t64{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5widgets5t64{a} libqt5xml5t64{a} libraqm0{a} librav1e0.7{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libsqlite3-dev{a} libssh2-1t64{a} libstdc++-14-dev{a} libsvtav1enc2{a} libtasn1-6{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{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} libxdmcp6{a} libxext6{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2-16{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} libzopfli1{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} netbase{a} openstructure{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-attr{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-fs{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-numpy-dev{a} python3-ost{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-platformdirs{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-sympy{a} python3-tk{a} python3-ufolib2{a} python3-unicodedata2{a} python3-zopfli{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xkb-data{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common krb5-locales libarchive-cpio-perl libcifpp-data libglib2.0-data libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pooch python3-yaml qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 307 newly installed, 0 to remove and 0 not upgraded. Need to get 356 MB of archives. After unpacking 1327 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 91 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.4-2 [190 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.12.1-1 [1871 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-9+b2 [946 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1916.20250814-1 [172 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.3.0-1 [135 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 126 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-5 [336 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-5 [352 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-5 [265 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-5 [385 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 134 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-5 [313 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-5 [337 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 145 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-5 [488 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-5 [560 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 148 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-4 [267 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.1-1 [41.8 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 153 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.125-2 [64.1 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.7-6 [25.9 MB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 25.2.3-1 [10.3 MB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 25.2.3-1 [46.0 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.24.0-2+b1 [28.5 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 25.2.3-1 [123 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.4+dfsg-1 [32.4 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.55-2 [88.1 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.4.321.0-1 [133 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 25.2.3-1 [47.6 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 25.2.3-1 [116 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.4-3 [1518 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-7 [76.3 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-7 [14.6 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 11.5.0-1 [517 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.16.1-1 [112 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.16.1-1 [26.8 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.28.1-1 [26.3 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.7-1 [22.6 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.28.1-1 [143 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libost-base2.9 amd64 2.9.3-2 [34.9 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libost-base-dev amd64 2.9.3-2 [29.1 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libost-geom2.9 amd64 2.9.3-2 [66.4 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libost-mol2.9 amd64 2.9.3-2 [395 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.17+dfsg-3 [2017 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.17+dfsg-3 [136 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libost-info2.9 amd64 2.9.3-2 [168 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libost-seq2.9 amd64 2.9.3-2 [91.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libost-bindings2.9 amd64 2.9.3-2 [204 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libost-conop2.9 amd64 2.9.3-2 [190 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libost-conop-dev amd64 2.9.3-2 [23.5 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libost-db2.9 amd64 2.9.3-2 [45.6 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libost-geom-dev amd64 2.9.3-2 [30.1 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libost-img2.9 amd64 2.9.3-2 [144 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libost-img-alg2.9 amd64 2.9.3-2 [170 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libost-gfx2.9 amd64 2.9.3-2 [433 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg2.9 amd64 2.9.3-2 [370 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-5 [364 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libost-io2.9 amd64 2.9.3-2 [884 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libparasail8 amd64 2.6.2+dfsg-2 [1890 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg2.9 amd64 2.9.3-2 [255 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.17+dfsg-3 [235 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.17+dfsg-3 [756 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.1-1 [23.5 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [16.7 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.10-1 [18.4 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-2.1 [113 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2.1 [16.2 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.17+dfsg-3 [3767 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.17+dfsg-3 [2591 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libost-gui2.9 amd64 2.9.3-2 [507 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libost-img-dev amd64 2.9.3-2 [44.6 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libost-info-dev amd64 2.9.3-2 [21.9 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libost-io-dev amd64 2.9.3-2 [53.5 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg-dev amd64 2.9.3-2 [32.6 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libost-mol-dev amd64 2.9.3-2 [59.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm2.9 amd64 2.9.3-2 [299 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm-dev amd64 2.9.3-2 [29.8 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg-dev amd64 2.9.3-2 [179 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libost-seq-dev amd64 2.9.3-2 [26.0 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.17-3 [2760 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.17+dfsg-3 [135 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.17-3 [150 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.17+dfsg-3 [220 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.17+dfsg-3 [161 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-8 [1172 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.10.1+dfsg1-5 [2737 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.7-1 [108 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 6.0.1-1 [1434 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.4+dfsg-1 [25.4 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.3.0-1 [69.5 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 16.0.0+ds-1 [324 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-5 [23.8 MB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.17.0-1+b1 [61.6 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-2+b2 [2801 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.9.3-2 [3990 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.9.3-2 [93.1 MB] Fetched 356 MB in 8s (43.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../032-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../033-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../034-libx11-data_2%3a1.8.12-1_all.deb ... Unpacking libx11-data (2:1.8.12-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../035-libx11-6_2%3a1.8.12-1_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.12-1) ... Selecting previously unselected package libxrender1:amd64. Preparing to unpack .../036-libxrender1_1%3a0.9.12-1_amd64.deb ... Unpacking libxrender1:amd64 (1:0.9.12-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../037-libxft2_2.3.6-1+b4_amd64.deb ... 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Setting up x11-common (1:7.7+25) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libgcrypt20:amd64 (1.11.2-2) ... Setting up libqhull-r8.0:amd64 (2020.2-7) ... Setting up libxcb-render-util0:amd64 (0.3.10-1) ... Setting up xkb-data (2.42-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libxcb-icccm4:amd64 (0.4.2-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-5) ... Setting up libabsl20240722:amd64 (20240722.0-4) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libpcre2-16-0:amd64 (10.46-1) ... 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Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb-xinerama0:amd64 (1.17.0-2+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libzopfli1 (1.0.3-3) ... Setting up libsqlite3-dev:amd64 (3.46.1-8) ... Setting up libx11-data (2:1.8.12-1) ... Setting up libsvtav1enc2:amd64 (2.3.0+dfsg-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up libjsoncpp26:amd64 (1.9.6-4) ... Setting up libavahi-common-data:amd64 (0.8-17) ... Setting up libdbus-1-3:amd64 (1.16.2-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (4.4.0-3) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up fonts-dejavu-mono (2.37-8) ... 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Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up libstdc++-14-dev:amd64 (14.3.0-8) ... Setting up libdrm-common (2.4.125-2) ... Setting up libyuv0:amd64 (0.0.1916.20250814-1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up libevdev2:amd64 (1.13.4+dfsg-1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libost-geom2.9:amd64 (2.9.3-2) ... Setting up libwacom-common (2.16.1-1) ... Setting up libxkbcommon0:amd64 (1.7.0-2.1) ... Setting up libwayland-client0:amd64 (1.24.0-2+b1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19 (1:19.1.7-6) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up libavif16:amd64 (1.3.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libboost1.83-dev:amd64 (1.83.0-5) ... Setting up gettext (0.23.1-2+b1) ... Setting up libxrender1:amd64 (1:0.9.12-1) ... Setting up libtool (2.5.4-5) ... Setting up fontconfig-config (2.15.0-2.4) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libboost-program-options1.83-dev:amd64 (1.83.0-5) ... Setting up libavahi-common3:amd64 (0.8-17) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libboost-test-dev:amd64 (1.83.0.2+b2) ... Setting up dh-autoreconf (21) ... Setting up libglib2.0-0t64:amd64 (2.84.4-3) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libboost-program-options-dev:amd64 (1.83.0.2+b2) ... Setting up libost-mol2.9 (2.9.3-2) ... Setting up shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libxkbcommon-x11-0:amd64 (1.7.0-2.1) ... Setting up libeigen3-dev (3.4.0-5) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libboost-atomic1.83-dev:amd64 (1.83.0-5) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up groff-base (1.23.0-9) ... Setting up libharfbuzz0b:amd64 (11.5.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b3) ... Setting up libfontconfig1:amd64 (2.15.0-2.4) ... Setting up libboost-system1.83-dev:amd64 (1.83.0-5) ... Setting up libost-geom-dev (2.9.3-2) ... Setting up libsm6:amd64 (2:1.2.6-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libicu-dev:amd64 (76.1-4) ... Setting up libavahi-client3:amd64 (0.8-17) ... Setting up libost-conop2.9 (2.9.3-2) ... Setting up libgudev-1.0-0:amd64 (238-7) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up fontconfig (2.15.0-2.4) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b4) ... Setting up python3.13 (3.13.7-1) ... Setting up libwacom9:amd64 (2.16.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.17-1) ... Setting up libdrm-intel1:amd64 (2.4.125-2) ... Setting up libost-mol-dev (2.9.3-2) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up libboost-filesystem1.83-dev:amd64 (1.83.0-5) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.13-tk (3.13.7-1) ... Setting up python3-platformdirs (4.4.0-1) ... Setting up python3-zopfli (0.2.3.post1-1+b1) ... Setting up libinput-bin (1.28.1-1) ... Setting up libost-conop-dev (2.9.3-2) ... Setting up python3-fs (2.4.16-8) ... Setting up libqt5core5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up python3-brotli (1.1.0-2+b7) ... Setting up libraqm0:amd64 (0.10.3-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-cycler (0.12.1-2) ... Setting up python3-kiwisolver (1.4.7-3+b1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-5) ... Setting up python3-numpy (1:2.2.4+ds-1.2) ... Setting up python3-pyqt5.sip (12.17.0-1+b1) ... Setting up python3-lxml:amd64 (6.0.1-1) ... Setting up libqt5sql5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-dateutil (2.9.0-4) ... Setting up python3-contourpy (1.3.1-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up libcups2t64:amd64 (2.4.10-4) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up dh-python (6.20250414) ... Setting up libinput10:amd64 (1.28.1-1) ... Setting up python3-sympy (1.14.0-2) ... Setting up python3-attr (25.3.0-1) ... Setting up mesa-libgallium:amd64 (25.2.3-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up libqt5dbus5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-scipy (1.15.3-1.1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up libcurl4t64:amd64 (8.16.0-1) ... Setting up libgbm1:amd64 (25.2.3-1) ... Setting up python3-lz4 (4.4.4+dfsg-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-5) ... Setting up python3-unicodedata2 (16.0.0+ds-1) ... Setting up blt (2.5.3+dfsg-8) ... Setting up libgl1-mesa-dri:amd64 (25.2.3-1) ... Setting up libqt5network5t64:amd64 (5.15.17+dfsg-3) ... Setting up libqt5xml5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-tk:amd64 (3.13.5-1) ... Setting up debhelper (13.26) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libqt5test5t64:amd64 (5.15.17+dfsg-3) ... Setting up python3-pil:amd64 (11.3.0-1) ... Setting up libegl-mesa0:amd64 (25.2.3-1) ... Setting up python3-pil.imagetk:amd64 (11.3.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up libboost-python1.83-dev (1.83.0-5) ... Setting up libegl1:amd64 (1.7.0-1+b2) ... Setting up cmake (4.1.1+really3.31.6-2) ... Setting up libost-info2.9 (2.9.3-2) ... Setting up libglx-mesa0:amd64 (25.2.3-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up libost-info-dev (2.9.3-2) ... Setting up libost-seq2.9 (2.9.3-2) ... Setting up libost-img2.9 (2.9.3-2) ... Setting up libost-seq-dev (2.9.3-2) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libost-img-alg2.9 (2.9.3-2) ... Setting up libost-seq-alg2.9 (2.9.3-2) ... Setting up libost-bindings2.9 (2.9.3-2) ... Setting up libost-db2.9 (2.9.3-2) ... Setting up libost-img-dev (2.9.3-2) ... Setting up libost-mol-alg2.9 (2.9.3-2) ... Setting up libost-seq-alg-dev (2.9.3-2) ... Setting up libost-gfx2.9 (2.9.3-2) ... Setting up libqt5gui5t64:amd64 (5.15.17+dfsg-3) ... Setting up libost-mol-alg-dev (2.9.3-2) ... Setting up libost-io2.9 (2.9.3-2) ... Setting up libqt5widgets5t64:amd64 (5.15.17+dfsg-3) ... Setting up libost-mol-mm2.9 (2.9.3-2) ... Setting up libost-mol-mm-dev (2.9.3-2) ... Setting up libqt5help5:amd64 (5.15.17-3) ... Setting up libost-gui2.9 (2.9.3-2) ... Setting up libost-io-dev (2.9.3-2) ... Setting up libqt5printsupport5t64:amd64 (5.15.17+dfsg-3) ... Setting up libqt5designer5:amd64 (5.15.17-3) ... Setting up python3-pyqt5 (5.15.11+dfsg-2+b2) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-5) ... Setting up python3-ost (2.9.3-2) ... Setting up openstructure (2.9.3-2) ... Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../promod3_3.4.2+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.2+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_configure -- \ -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DOPTIMIZE=ON -DDISABLE_DOCUMENTATION=ON -DOST_ROOT=/usr -DCOMPOUND_LIB=/var/cache/openstructure/compounds.chemlib .. -- The CXX compiler identification is GNU 15.2.0 -- The C compiler identification is GNU 15.2.0 -- 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 CMake Warning (dev) at CMakeLists.txt:58 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- 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 CMake Warning (dev) at cmake_support/PROMOD3.cmake:980 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:997 (get_compiler_version) CMakeLists.txt:87 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.13.7", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed CMake Warning (dev) at cmake_support/PROMOD3.cmake:1029 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost package: python313 CMake Warning (dev) at cmake_support/PROMOD3.cmake:1043 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: unit_test_framework CMake Warning (dev) at cmake_support/PROMOD3.cmake:1050 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: filesystem system CMake Warning (dev) at cmake_support/PROMOD3.cmake:1054 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: iostreams CMake Warning (dev) at cmake_support/PROMOD3.cmake:1057 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: program_options CMake Warning (dev) at cmake_support/PROMOD3.cmake:1060 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:98 (setup_boost) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: regex -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): config/src/CMakeLists.txt:8 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:593 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/init/CMakeLists.txt:9 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) core/src/CMakeLists.txt:33 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): core/pymod/CMakeLists.txt:15 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) core/tests/CMakeLists.txt:41 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) loop/src/CMakeLists.txt:52 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): loop/pymod/CMakeLists.txt:21 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) loop/tests/CMakeLists.txt:33 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) scoring/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scoring/pymod/CMakeLists.txt:16 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) scoring/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) sidechain/src/CMakeLists.txt:56 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): sidechain/pymod/CMakeLists.txt:22 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) sidechain/tests/CMakeLists.txt:11 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:315 (copy_if_different) cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:317 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:292 (stage_and_install_headers) modelling/src/CMakeLists.txt:50 (module) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:553 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:641 (copy_if_different) modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:645 (install): Policy CMP0177 is not set: install() DESTINATION paths are normalized. Run "cmake --help-policy CMP0177" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): modelling/pymod/CMakeLists.txt:35 (pymod) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) modelling/tests/CMakeLists.txt:76 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:464 (copy_if_different) scripts/CMakeLists.txt:12 (script) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): scripts/CMakeLists.txt:15 (copy_if_different) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:724 (copy_if_different) actions/tests/CMakeLists.txt:14 (promod3_unittest) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:6 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:7 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:8 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake_support/PROMOD3.cmake:142 (add_custom_command): The following keywords are not supported when using add_custom_command(TARGET): DEPENDS. Policy CMP0175 is not set: add_custom_command() rejects invalid arguments. Run "cmake --help-policy CMP0175" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:1230 (copy_if_different) actions/CMakeLists.txt:9 (pm_action) This warning is for project developers. Use -Wno-dev to suppress it. -- ProMod3 will be built with the following options: OpenStructure (-DOST_ROOT) : /usr Compound library (-DCOMPOUND_LIB): /var/cache/openstructure/compounds.chemlib Optimized (-DOPTIMIZE) : ON Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 -- Configuring done (2.2s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Generating ../stage/etc/bash_completion.d/pm-completion.bash make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake [ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 [ 1%] Built target loop_data_dir [ 1%] Built target sidechain_pymod [ 1%] Built target scoring_data_dir cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help [ 1%] Built target loop_pymod [ 1%] Built target config_header [ 1%] Built target sidechain_data_dir [ 1%] Built target scoring_pymod make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target subst_pm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains [ 1%] Built target bash-completion make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build [ 1%] Built target init___init__.py_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend [ 1%] Built target core_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm [ 1%] Built target actions make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh [ 1%] Built target init_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py [ 1%] Built target promod3_scripts cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh [ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh [ 1%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o [ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh [ 5%] Built target promod3_modelling_headers cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh [ 5%] Built target promod3_loop_headers cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_sidechain_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_scoring_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_core.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.4 -o ../../stage/lib64/libpromod3_core.so.3.4.2 CMakeFiles/promod3_core.dir/cluster.cc.o CMakeFiles/promod3_core.dir/geom_base.cc.o CMakeFiles/promod3_core.dir/geom_stems.cc.o CMakeFiles/promod3_core.dir/superpose.cc.o CMakeFiles/promod3_core.dir/graph.cc.o CMakeFiles/promod3_core.dir/tree.cc.o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_core.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4 ../../stage/lib64/libpromod3_core.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_core make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/wrap_core.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_env.cc [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_geom.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/all_atom_positions.cc [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/amino_acid_atoms.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_runtime_profiling.cc [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o cd 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/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/backbone.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/bb_trace_param.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/density_creator.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o 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CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_constructor.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/fragger.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -MF CMakeFiles/promod3_loop.dir/idx_handler.cc.o.d -o CMakeFiles/promod3_loop.dir/idx_handler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/idx_handler.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_rule_lookup.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -MF CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o.d -o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -MF CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/mm_system_creator.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/psipred_prediction.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -MF CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o.d -o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/torsion_sampler.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_rule_lookup.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_core.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:22, from /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, 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++/15/bits/basic_string.h:991:15, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:1165:19: 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] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /usr/include/boost/variant.hpp:17, from /usr/include/ost/generic_property.hh:34, from /usr/include/ost/mol/entity_base.hh:25, from /usr/include/ost/mol/entity_view.hh:27, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:29: /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/15/string:44: In static member function 'static 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++/15/bits/basic_string.h:451:23, 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++/15/bits/basic_string.h:969:18, 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/char_traits.h:352:16: 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] 352 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /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>& 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]', 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:2338:48, 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:2350:43, 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:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/15/bits/basic_string.h:992:24: warning: '*(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::.std::__cxx11::basic_string::::_M_allocated_capacity' may be used uninitialized [-Wmaybe-uninitialized] 992 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 19%] Linking CXX shared library ../../stage/lib64/libpromod3_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_loop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_loop.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_loop.so.3.4 -o ../../stage/lib64/libpromod3_loop.so.3.4.2 CMakeFiles/promod3_loop.dir/all_atom_env.cc.o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o CMakeFiles/promod3_loop.dir/backbone.cc.o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o CMakeFiles/promod3_loop.dir/density_creator.cc.o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o CMakeFiles/promod3_loop.dir/frag_db.cc.o CMakeFiles/promod3_loop.dir/fragger.cc.o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/idx_handler.cc.o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o CMakeFiles/promod3_loop.dir/structure_db.cc.o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4 ../../stage/lib64/libpromod3_loop.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 19%] Built target promod3_loop make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src 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scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_amino_acid_atoms.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_score_base.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc [ 25%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc [ 25%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc [ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_positions.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cb_packing_score.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o [ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_overall_scorer.cc [ 28%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/bb_dep_rotamer_lib.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/disulfid.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_fragger.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_loop_object_loader.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc [ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/particle_scoring.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_particle_scoring.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_particle_scoring.cc [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_env_listener.cc [ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_score.cc [ 33%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc [ 33%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_particle_scoring.cc [ 35%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc [ 36%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer.cc [ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc [ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_cruncher.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/density_score.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc [ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_density.cc [ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_group.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_id.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib.cc [ 42%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_entry.cc [ 42%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc [ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc [ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/constraint_constructor.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_overall_scorer.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:17: In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = bool]', inlined from 'boost::python::extract::operator result_type() const [with T = bool]' at /usr/include/boost/python/extract.hpp:136:23, inlined from 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: /usr/include/boost/python/extract.hpp:185:11: warning: '*(bool*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertListToVector(const boost::python::list&, std::vector&) [with T = bool]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: note: '' declared here 66 | v.push_back(boost::python::extract(l[i])); | ^~~~~~~~~~~~~~~~ [ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_rotamer_constructor.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_packing_score.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_clash_score.cc [ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_rotamer_constructor.cc [ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_rotamer_constructor.cc [ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/subrotamer_optimizer.cc [ 53%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_loop.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 53%] Built target _loop [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_scoring.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_scoring.so.3.4 -o ../../stage/lib64/libpromod3_scoring.so.3.4.2 CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o CMakeFiles/promod3_scoring.dir/clash_score.cc.o CMakeFiles/promod3_scoring.dir/density_score.cc.o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4 ../../stage/lib64/libpromod3_scoring.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 53%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o 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CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_pairwise_functions.cc [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_density_scorer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_scwrl3_energy_functions.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -MF CMakeFiles/_scoring.dir/export_object_loader.cc.o.d -o CMakeFiles/_scoring.dir/export_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_object_loader.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/wrap_scoring.cc [ 60%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_sidechain.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.2 CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o CMakeFiles/promod3_sidechain.dir/frame.cc.o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4 ../../stage/lib64/libpromod3_sidechain.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 60%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/extension_scheme.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_graph.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap_extender.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/model.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/all_atom_relaxer.cc [ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc [ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_cruncher.cc [ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/ccd.cc [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/loop_candidate.cc [ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_density.cc [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_all_atom_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_ids.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_lib.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_sidechain_object_loader.cc [ 74%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_constructor.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_cooler.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc [ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_subrotamer_optimizer.cc [ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/wrap_sidechain.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/rigid_blocks.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_reconstructor.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_env_listener.cc 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:18: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/afdb.cc [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_scoring.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/scoring/_scoring.so CMakeFiles/_scoring.dir/export_backbone_score.cc.o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o CMakeFiles/_scoring.dir/export_object_loader.cc.o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o CMakeFiles/_scoring.dir/export_density_scorer.cc.o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _scoring In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc:17: /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 4 of type 'const double*' 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 = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 81%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o CMakeFiles/_sidechain.dir/export_particle.cc.o CMakeFiles/_sidechain.dir/export_rotamer.cc.o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_modelling.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_modelling.so.3.4 -o ../../stage/lib64/libpromod3_modelling.so.3.4.2 CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o CMakeFiles/promod3_modelling.dir/gap.cc.o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o CMakeFiles/promod3_modelling.dir/model.cc.o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o CMakeFiles/promod3_modelling.dir/ccd.cc.o CMakeFiles/promod3_modelling.dir/kic.cc.o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o CMakeFiles/promod3_modelling.dir/score_container.cc.o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o CMakeFiles/promod3_modelling.dir/afdb.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_modelling.so.3.4 ../../stage/lib64/libpromod3_modelling.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 81%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o -MF CMakeFiles/_modelling.dir/export_gap_extender.cc.o.d -o CMakeFiles/_modelling.dir/export_gap_extender.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_gap_extender.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -MF CMakeFiles/_modelling.dir/export_loop_candidate.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_loop_candidate.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -MF CMakeFiles/_modelling.dir/export_model.cc.o.d -o CMakeFiles/_modelling.dir/export_model.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_model.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_rigid_blocks.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -MF CMakeFiles/_modelling.dir/export_extension_scheme.cc.o.d -o CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_extension_scheme.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -MF CMakeFiles/_modelling.dir/export_scoring_weights.cc.o.d -o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_afdb.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_loop_closure.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -MF CMakeFiles/_modelling.dir/export_monte_carlo.cc.o.d -o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_sidechain_reconstructor.cc [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o -MF CMakeFiles/_modelling.dir/export_gap.cc.o.d -o CMakeFiles/_modelling.dir/export_gap.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_gap.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -MF CMakeFiles/_modelling.dir/export_motif_finder.cc.o.d -o CMakeFiles/_modelling.dir/export_motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_motif_finder.cc [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:16, from /usr/include/boost/function/function_template.hpp:13, from /usr/include/boost/function/detail/maybe_include.hpp:15, from /usr/include/boost/function/function0.hpp:11, from /usr/include/boost/python/errors.hpp:13, from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:13: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:21: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:112:39: note: '' declared here 112 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:179:39: note: '' declared here 179 | String seq = extract(args[0]); | ^ 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, inlined from 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)' at /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc:47:39: note: '' declared here 47 | String seq = extract(args[0]); | ^ [ 90%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_modelling.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib64/python3.13/site-packages/promod3/modelling/_modelling.so CMakeFiles/_modelling.dir/export_extension_scheme.cc.o CMakeFiles/_modelling.dir/export_gap.cc.o CMakeFiles/_modelling.dir/export_gap_extender.cc.o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o CMakeFiles/_modelling.dir/export_loop_closure.cc.o CMakeFiles/_modelling.dir/export_model.cc.o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o CMakeFiles/_modelling.dir/export_score_container.cc.o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o CMakeFiles/_modelling.dir/export_motif_finder.cc.o CMakeFiles/_modelling.dir/export_afdb.cc.o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_modelling.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make 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/build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler [ 94%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 94%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup [ 95%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat [ 97%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat [ 97%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat [ 97%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer [ 97%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer [ 97%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer [ 98%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_cbeta_scorer.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" [100%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_cb_packing_scorer.dat [100%] Built target generate_scoring_data_hbond_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_ss_agreement_scorer.dat [100%] Built target generate_scoring_data_aa_scorer.dat [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat [100%] Built target generate_loop_data_ff_lookup_charmm.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' Compound library not available. Some functionality may not work as expected. [100%] Built target generate_scoring_data_reduced_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_extended.dat [100%] Built target generate_loop_data_torsion_sampler_helical.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_coil.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler.dat [100%] Built target generate_sidechain_data_bb_dep_lib.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 check ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target actions make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/tests/data/seq_ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 0%] Built target test_data_actions make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] running checks test_actions.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_actions.py" Compound library not available. Some functionality may not work as expected. . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_actions.py_run make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests//test_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/broken_on_purpose.chemlib /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.json /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/alignment.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_1.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_2trg.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_3.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake.fas.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_nel.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/tests/data/fasta/1ake_sw.fas /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target test_data_core make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target promod3_core_headers make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/src/CMakeFiles/promod3_core.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 4%] Built target promod3_core make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 4%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_check_io.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_portable_binary.cc [ 5%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_graph_minimizer.cc [ 6%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/tests/tests.cc [ 6%] Linking CXX executable ../../tests/core/test_suite_core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_core.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_core.dir/link.d CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target test_suite_core make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 6%] Built target core_pymod make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/pymod/CMakeFiles/_core.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 8%] Built target _core make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] running checks for module core cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core/test_suite_core Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 9%] Built target test_suite_core_run make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] running checks test_setcompoundschemlib.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_setcompoundschemlib.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.127s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 10%] Built target test_setcompoundschemlib.py_run make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_helper.py" Compound library not available. Some functionality may not work as expected. ............ ---------------------------------------------------------------------- Ran 12 tests in 0.002s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_helper.py_run make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_pm3argparse.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/core/tests/test_pm3argparse.py" Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- Ran 66 tests in 1.535s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target test_pm3argparse.py_run make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target loop_data_dir make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target modelling_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 11%] Built target promod3_loop_headers make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/src/CMakeFiles/promod3_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target promod3_loop make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 20%] Built target loop_pymod make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/pymod/CMakeFiles/_loop.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target _loop make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 25%] Built target promod3_scoring_headers make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 36%] Built target scoring_pymod make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/pymod/CMakeFiles/_scoring.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target _scoring make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 40%] Built target promod3_sidechain_headers make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/src/CMakeFiles/promod3_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 51%] Built target sidechain_pymod make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/pymod/CMakeFiles/_sidechain.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target _sidechain make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 57%] Built target promod3_modelling_headers make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/src/CMakeFiles/promod3_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 67%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'modelling/pymod/CMakeFiles/_modelling.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 73%] Built target _modelling make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target init_pymod make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 74%] Built target _init make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_ff_lookup_charmm.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 75%] Built target generate_loop_data_torsion_sampler_coil.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_extended.dat make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler_helical.dat make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_frag_db.dat make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target generate_loop_data_structure_db.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target loop_data make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1A88A_with_gap.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1akyA.horiz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/all_aa_prot_ref.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/tests/data/CHARMM27.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Built target test_data_loop make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 77%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c 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/usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop_run.dir/build.make loop/tests/CMakeFiles/test_suite_loop_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] running checks for module loop cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/loop/test_suite_loop Running 68 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target test_suite_loop_run make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 84%] Built target scoring_data_dir make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_aa_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 85%] Built target generate_scoring_data_cb_packing_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 86%] Built target generate_scoring_data_cbeta_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_reduced_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_hbond_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_ss_agreement_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_torsion_scorer.dat make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target scoring_data make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/1CRNA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/data/clash_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 87%] Built target test_data_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_score_base.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_backbone_scorer.cc [ 88%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/test_all_atom_scorer.cc:73:33: warning: 'promod3::loop::AllAtomPositions scoring::{anonymous}::GenerateTestPos(const String&, uint, uint)' defined but not used [-Wunused-function] 73 | promod3::loop::AllAtomPositions GenerateTestPos( | ^~~~~~~~~~~~~~~ [ 89%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/tests/tests.cc [ 89%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_scoring.dir/link.d CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o CMakeFiles/test_suite_scoring.dir/tests.cc.o -o ../../tests/scoring/test_suite_scoring -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 89%] Built target test_suite_scoring make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build.make scoring/tests/CMakeFiles/test_suite_scoring_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] running checks for module scoring cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/scoring/test_suite_scoring Running 20 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target test_suite_scoring_run make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 90%] Built target sidechain_data_dir make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target generate_sidechain_data_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target sidechain_data make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/data/all_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_data_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 91%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_frame_construction.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/test_rotamers.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o -MF CMakeFiles/test_suite_sidechain.dir/tests.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests/tests.cc [ 93%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_sidechain.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_sidechain.dir/link.d CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -o ../../tests/sidechain/test_suite_sidechain -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] running checks for module sidechain cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/sidechain/test_suite_sidechain Running 4 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_suite_sidechain_run make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1cjx-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_build.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_final.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1crn_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1CRNA.hhm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_rec.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1eye_sc_test.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/1mcg.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2dbs.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2jlp-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/2xim-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/3b08-3.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.pdb.gz /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/4ksl-1.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/CA-3cm91E.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/cbeta.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/del.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ff_NAD.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_almost_on_top.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/gly_shifted_nter.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/hetero-punched.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ins.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/neighbor-punched.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/port_frag_db.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/port_str_db.dat /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/sep.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/smtl2bl4.1.pdb /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/ter.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/data/double_gap_aln.fasta /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 93%] Built target test_data_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_candidates.cc [ 94%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_loop_closing.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstructor.cc [ 95%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o -MF CMakeFiles/test_suite_modelling.dir/tests.cc.o.d -o CMakeFiles/test_suite_modelling.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/tests.cc [ 95%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_modelling.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_suite_modelling.dir/link.d CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_modelling.so.3.4.2 ../../stage/lib64/libpromod3_scoring.so.3.4.2 ../../stage/lib64/libpromod3_sidechain.so.3.4.2 ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 95%] Built target test_suite_modelling make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build.make modelling/tests/CMakeFiles/test_suite_modelling_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks for module modelling cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling/test_suite_modelling Running 7 test cases... *** No errors detected make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_suite_modelling_run make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build.make modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_close_gaps.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_close_gaps.py" Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- Ran 33 tests in 18.709s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_close_gaps.py_run make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build.make modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_gap_extension.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_gap_extension.py" Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- Ran 6 tests in 0.017s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 96%] Built target test_gap_extension.py_run make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_modelling.py_run.dir/build.make modelling/tests/CMakeFiles/test_modelling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_modelling.py" Compound library not available. Some functionality may not work as expected. ..............Alignment-structure mismatch at pos 0 in chain A, alignment is 'X' structure residue is 'S'. Ok for modified residue SEP. ...residue A.GLY8 has conflicting atom CA - skipping atom. residue A.GLY8 is missing atoms CA ........ ---------------------------------------------------------------------- Ran 25 tests in 0.103s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_modelling.py_run make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build.make modelling/tests/CMakeFiles/test_pipeline.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_pipeline.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_pipeline.py" Compound library not available. Some functionality may not work as expected. Switched to slower reference platform of OpenMM! ............... ---------------------------------------------------------------------- Ran 15 tests in 30.975s OK OpenMM CPU platform not available. Skipping almost_on_top check. phenix.molprobity is missing. Please install it and make it available in your PATH to execute test testMolProbity. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_pipeline.py_run make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_ring_punches.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_ring_punches.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.108s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 97%] Built target test_ring_punches.py_run make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build.make modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_sidechain_reconstruction.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_sidechain_reconstruction.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 2.034s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_sidechain_reconstruction.py_run make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build.make modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/modelling/tests/test_alignment_fiddling.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.010s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_alignment_fiddling.py_run make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target subst_pm make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target promod3_scripts make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-model.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-model.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-model.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 5.328s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-model.py_run make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build.make actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-rawmodel.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_build-rawmodel.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 1.670s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_action_build-rawmodel.py_run make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] running checks test_action_help.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.2+ds/actions/tests/test_action_help.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.036s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target test_action_help.py_run make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target codetest make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_core.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./check_io.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./cluster.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./dynamic_spatial_organizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./export_helper.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./geom_stems.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./message.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_sink.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_source.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./portable_binary_serializer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./runtime_profiling.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./superpose.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./enumerator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tree.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./tetrahedral_polytope.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./graph_minimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/core/./eigen_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/_core.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/core/pm3argparse.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_loop.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_env.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./all_atom_positions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./amino_acid_atoms.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./backbone.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./bb_trace_param.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./data_bag.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_hash_table.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Up-to-date: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./density_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./forcefield_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./frag_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./fragger.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./idx_handler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./loop_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./mm_system_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./psipred_prediction.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./stem_geom.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./torsion_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./ushort_vec.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/loop/./structure_db_custom_types.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/loop/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_scoring.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./backbone_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scoring_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cb_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./reduced_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./density_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./hbond_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./torsion_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_scoring_function.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./constraint_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/scoring/./scwrl3_energy_functions.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/scoring/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./disulfid.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./frame.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_graph.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring_base.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_cruncher.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_density.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_group.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_id.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_entry.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_reader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_connector.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./vina_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/sidechain/./subrotamer_optimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/sidechain/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2 -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.2" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/libpromod3_modelling.so -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./extension_scheme.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./gap_extender.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./model.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./all_atom_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./backbone_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./ccd.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./kic.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./loop_candidate.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_closer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_cooler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./rigid_blocks.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./score_container.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./scoring_weights.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_reconstructor.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./motif_finder.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./robin_hood.h -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/include/promod3/modelling/./afdb.hh -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_denovo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_planar_rings.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/bin/pm -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/reproducible-path/promod3-3.4.2+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install for PKG in core loop modelling scoring sidechain; do \ dh_install -p libpromod3-${PKG}-dev usr/include/promod3/${PKG}; \ dh_install -p libpromod3-${PKG}-dev usr/lib64/libpromod3_${PKG}.so usr/lib/x86_64-linux-gnu; \ dh_install -p libpromod3-${PKG}3.4 usr/lib64/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib64 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:421: renaming _modelling.so to _modelling.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _loop.so to _loop.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package promod3: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.2+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.4.2+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.4.2+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3517703 and its subdirectories I: Current time: Thu Oct 22 19:02:58 +14 2026 I: pbuilder-time-stamp: 1792645378 + false + set +x Thu Oct 22 05:02:58 UTC 2026 I: Signing ./b2/promod3_3.4.2+ds-1_amd64.buildinfo as promod3_3.4.2+ds-1_amd64.buildinfo.asc Thu Oct 22 05:02:58 UTC 2026 I: Signed ./b2/promod3_3.4.2+ds-1_amd64.buildinfo as ./b2/promod3_3.4.2+ds-1_amd64.buildinfo.asc Thu Oct 22 05:02:58 UTC 2026 - build #2 for promod3/unstable/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Thu Oct 22 05:02:58 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-8PY1Urxr, removing. /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw: total 944 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 22:25 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 22:40 b2 -rw-rw-r-- 1 jenkins jenkins 3240 Apr 1 10:00 promod3_3.4.2+ds-1.dsc -rw------- 1 jenkins jenkins 948253 Sep 18 22:25 rbuildlog.tdEmpvo /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1: total 803548 -rw-r--r-- 1 jenkins jenkins 943605 Sep 18 22:25 build.log -rw-r--r-- 1 jenkins jenkins 24480 Sep 18 22:25 libpromod3-core-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2656392 Sep 18 22:25 libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 95292 Sep 18 22:25 libpromod3-core3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 35500 Sep 18 22:25 libpromod3-loop-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5353248 Sep 18 22:25 libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 290316 Sep 18 22:25 libpromod3-loop3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 37152 Sep 18 22:25 libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12137636 Sep 18 22:25 libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 307252 Sep 18 22:25 libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 18072 Sep 18 22:25 libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4526828 Sep 18 22:25 libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 181792 Sep 18 22:25 libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19428 Sep 18 22:25 libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4495028 Sep 18 22:25 libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 238772 Sep 18 22:25 libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 371418628 Sep 18 22:25 promod3-data_3.4.2+ds-1_all.deb -rw-r--r-- 1 jenkins jenkins 5884 Sep 18 22:25 promod3_3.4.2+ds-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3240 Sep 18 22:25 promod3_3.4.2+ds-1.dsc -rw-r--r-- 1 jenkins jenkins 11036 Sep 18 22:25 promod3_3.4.2+ds-1_all.deb -rw-r--r-- 1 jenkins jenkins 18989 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 19871 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 7769 Sep 18 22:25 promod3_3.4.2+ds-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 1470 Sep 18 22:25 promod3_3.4.2+ds-1_source.changes -rw-r--r-- 1 jenkins jenkins 398726492 Sep 18 22:25 promod3_3.4.2+ds.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 19269372 Sep 18 22:25 python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1060036 Sep 18 22:25 python3-promod3_3.4.2+ds-1_amd64.deb /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2: total 802828 -rw-rw-r-- 1 jenkins jenkins 944489 Sep 18 22:39 build.log -rw-r--r-- 1 jenkins jenkins 24480 Sep 18 22:39 libpromod3-core-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 2656392 Sep 18 22:39 libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 95292 Sep 18 22:39 libpromod3-core3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 35500 Sep 18 22:39 libpromod3-loop-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 5353248 Sep 18 22:39 libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 290316 Sep 18 22:39 libpromod3-loop3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 37152 Sep 18 22:39 libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 12137636 Sep 18 22:39 libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 307252 Sep 18 22:39 libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 18072 Sep 18 22:39 libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4526828 Sep 18 22:39 libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 181792 Sep 18 22:39 libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 19428 Sep 18 22:39 libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 4495028 Sep 18 22:39 libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 238772 Sep 18 22:39 libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 371418628 Sep 18 22:40 promod3-data_3.4.2+ds-1_all.deb -rw-r--r-- 1 jenkins jenkins 5884 Sep 18 22:40 promod3_3.4.2+ds-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 3240 Sep 18 22:40 promod3_3.4.2+ds-1.dsc -rw-r--r-- 1 jenkins jenkins 11036 Sep 18 22:40 promod3_3.4.2+ds-1_all.deb -rw-rw-r-- 1 jenkins jenkins 18983 Sep 18 22:40 promod3_3.4.2+ds-1_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 19865 Sep 18 22:40 promod3_3.4.2+ds-1_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 7769 Sep 18 22:40 promod3_3.4.2+ds-1_amd64.changes -rw-rw-r-- 1 jenkins jenkins 1470 Sep 18 22:40 promod3_3.4.2+ds-1_source.changes -rw-r--r-- 1 jenkins jenkins 398726492 Sep 18 22:40 promod3_3.4.2+ds.orig.tar.xz -rw-r--r-- 1 jenkins jenkins 19269372 Sep 18 22:40 python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1060036 Sep 18 22:40 python3-promod3_3.4.2+ds-1_amd64.deb Thu Sep 18 22:40:05 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net. Thu Sep 18 22:40:06 UTC 2025 I: promod3_3.4.2+ds-1_amd64.changes: Format: 1.8 Date: Tue, 01 Apr 2025 05:15:30 -0400 Source: promod3 Binary: libpromod3-core-dev libpromod3-core3.4 libpromod3-core3.4-dbgsym libpromod3-loop-dev libpromod3-loop3.4 libpromod3-loop3.4-dbgsym libpromod3-modelling-dev libpromod3-modelling3.4 libpromod3-modelling3.4-dbgsym libpromod3-scoring-dev libpromod3-scoring3.4 libpromod3-scoring3.4-dbgsym libpromod3-sidechain-dev libpromod3-sidechain3.4 libpromod3-sidechain3.4-dbgsym promod3 promod3-data python3-promod3 python3-promod3-dbgsym Architecture: amd64 all Version: 3.4.2+ds-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libpromod3-core-dev - protein homology modelling engine libpromod3-core3.4 - protein homology modelling engine libpromod3-loop-dev - protein homology modelling engine libpromod3-loop3.4 - protein homology modelling engine libpromod3-modelling-dev - protein homology modelling engine libpromod3-modelling3.4 - protein homology modelling engine libpromod3-scoring-dev - protein homology modelling engine libpromod3-scoring3.4 - protein homology modelling engine libpromod3-sidechain-dev - protein homology modelling engine libpromod3-sidechain3.4 - protein homology modelling engine promod3 - protein homology modelling engine promod3-data - protein homology modelling engine - data files python3-promod3 - protein homology modelling engine - Python 3 package Changes: promod3 (3.4.2+ds-1) unstable; urgency=medium . * New upstream release 3.4.2+ds. Checksums-Sha1: 9d9469162228f6efd3ec8e6114611ce0a06906d6 24480 libpromod3-core-dev_3.4.2+ds-1_amd64.deb ae0f761a29b3aa389c002b1893020e1452b45627 2656392 libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb a1ad5e271d7f7cb8f1924d88747b86daca93994e 95292 libpromod3-core3.4_3.4.2+ds-1_amd64.deb 79026b7f60e7218c8926f7a16703f441b4e48c5a 35500 libpromod3-loop-dev_3.4.2+ds-1_amd64.deb 0e1634839674177bd6eee3dbd23fcfe2727460d3 5353248 libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb 9808bc0e31c72a18ceee03646022df2c84442a8e 290316 libpromod3-loop3.4_3.4.2+ds-1_amd64.deb 71c375ac07c4ec94f8ae5b8325c67272c0dc88d5 37152 libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb f5071aa8c8f5eaf6700b251e6f4c19268715346f 12137636 libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb 88867df2148ee55d1b37099e98ebc81b5d66f68f 307252 libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb e3ba19644efd3e66cad97bee0c00b81397497e24 18072 libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb 52defde017625c9e40422ee708387a7381baedfa 4526828 libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb 9baa7f30071f0c131157858ff34be9a22cb0000e 181792 libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb 287004a3d4b6ca68f4f1814800ed0021bc2239eb 19428 libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb e6e7030ecdc1f81adcaf0c252c4b8d06e9ead78c 4495028 libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb 7dfacf47cd1d99a5ddb9320af628bbec66a5c7d5 238772 libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb 1e11468ad525f2eacffe1a9d2ce31fb40c12f2fe 371418628 promod3-data_3.4.2+ds-1_all.deb f67ee4a18ec473bbaa5d8460c38fee94bbdb974b 11036 promod3_3.4.2+ds-1_all.deb 6273e98666572837669fe3a6b400309b64653df7 18989 promod3_3.4.2+ds-1_amd64.buildinfo 7b1d44177e49dfc9f8f53ac0922142bd59d71160 19269372 python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb 90624af23c53b4f176d73a99eaf4a96cce0c729a 1060036 python3-promod3_3.4.2+ds-1_amd64.deb Checksums-Sha256: 8724f179f94a17213a16613921ac4e6c938e4f95ec3ec8285e996806760c063c 24480 libpromod3-core-dev_3.4.2+ds-1_amd64.deb b1e754da8abe81b2b812b93251d8b457357dd2aab92230b98930565ec5f687c2 2656392 libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb 34f69c4fd995c229fbf35b1b998e9bb5cf8871d3b2a1f3b82626fde158aaa4cb 95292 libpromod3-core3.4_3.4.2+ds-1_amd64.deb 2d719f1333aaa9b28e8bea500621321e5247dc1a681d211a80e9c4e1d7e7c241 35500 libpromod3-loop-dev_3.4.2+ds-1_amd64.deb 2bb9df3ecb9e0d0ef02a5a3cda16ebfb1a95d344c4a1b5ca8a8b51de72b13deb 5353248 libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb 6f8979b50e182ff1f22e53da75a4656ac4d5cf4808c0c4c49af2b3573f46caba 290316 libpromod3-loop3.4_3.4.2+ds-1_amd64.deb d7ceaa7ea563a7ceccc5454fa4f19c7af244bf1f72c7e76744446c2417255731 37152 libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb 5762dc7e4f38982a5ac37ac33e56f98b783daab1f09162524c7fc7ca30a72161 12137636 libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb 0de49426a36ebe76f0ada4020af1bc97ca657fc3bccd3865b238a7aa9539743d 307252 libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb dcfeb2b8e05a5271afa5a482401ef81cd794355186214ccf9c9d222479bc9154 18072 libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb e58d100a07f4c3910a0b154857f9a36f4e6a957352fb316e2f01e8ab6b1382b3 4526828 libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb 4c123c4b9a70ef03c66c7f3a0e34dec80ce462d1dabcdc8bdf2b99b20b687d33 181792 libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb 307d3c329829efae338de18f114526fd02daca604ac1646ef2750c49023b5eb8 19428 libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb 388bc400a0f70489304ff145e2aef6fa0a1f75fe6f13ac5a2f2621adc11abd6d 4495028 libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb b2c3f754b4122f183d9bb85355f9871d2a36beb6549f639bf527c408e2f2c8ef 238772 libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb 1ac7c965c975bc4a6e39925f1ac2eea4b4b1195ec0f34948aabb5d91b356c08d 371418628 promod3-data_3.4.2+ds-1_all.deb 00e5160c165895f14f18933bbc3decbd80775be680587cede53ba489a8dc2a13 11036 promod3_3.4.2+ds-1_all.deb 258dabc2d62096df3f25b43b10387c839bf63a2181d702bd96d9d668be4578ae 18989 promod3_3.4.2+ds-1_amd64.buildinfo 146ac0964eb24b3cfadf38202084bc01928de71f8030eff6f74d0a5bb21fa27e 19269372 python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb 9fbd279935a3a0a0d627c90a8e3c683066374f779e914cc6b84eebc1e07e033c 1060036 python3-promod3_3.4.2+ds-1_amd64.deb Files: db42f2ce60de8b7fef829db4511b59d2 24480 libdevel optional libpromod3-core-dev_3.4.2+ds-1_amd64.deb 81b0bac971a94f8cb14aea845d614805 2656392 debug optional libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb 8c4dba14664c7a81b09944d6a549924f 95292 libs optional libpromod3-core3.4_3.4.2+ds-1_amd64.deb b87453f3ed58cb2e2dbe1edeccb47043 35500 libdevel optional libpromod3-loop-dev_3.4.2+ds-1_amd64.deb a1d5310ac526ae172087b6dd6c894cf2 5353248 debug optional libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb 0d01cf8a64d384fd51b38a6c17423f92 290316 libs optional libpromod3-loop3.4_3.4.2+ds-1_amd64.deb 1c4e395b8d0314de5a6fccc1931760bf 37152 libdevel optional libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb 38e0297b6ab94c268ff00db8291ca555 12137636 debug optional libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb 1f814b9dc27defd221dafdd1dc950f58 307252 libs optional libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb ae1fb51a5a3eea43ff300e6a98d6a424 18072 libdevel optional libpromod3-scoring-dev_3.4.2+ds-1_amd64.deb 61eb0d4dfda90fd2e8febaf441b89d64 4526828 debug optional libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb ef65627898cd176e35089c5a3ad3f12d 181792 libs optional libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb ab6aadec13d09ebe4818d5da7d04e3d2 19428 libdevel optional libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb ba7885c1cf4ab546348aefe2f68ed940 4495028 debug optional libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb fda4cdde7e3ef2feb298e90c10442955 238772 libs optional libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb f3ce7d831adf53849c6c14f891105250 371418628 science optional promod3-data_3.4.2+ds-1_all.deb 321d090a29825b8ff41cad4f7713cf1e 11036 science optional promod3_3.4.2+ds-1_all.deb e23027aa1522501042ea809c8478be08 18989 science optional promod3_3.4.2+ds-1_amd64.buildinfo c01ae3128cd0a5c6fc43d0257abe276d 19269372 debug optional python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb fda9641c8e5e7f02356fd29bb228d41f 1060036 python optional python3-promod3_3.4.2+ds-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/promod3_3.4.2+ds-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/promod3_3.4.2+ds-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/promod3_3.4.2+ds-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/promod3_3.4.2+ds-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/promod3_3.4.2+ds-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/promod3_3.4.2+ds-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 22:25:01.257473545 +0000 +++ b2/build.log 2025-09-18 22:39:59.118616614 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 18 10:09:30 -12 2025 -I: pbuilder-time-stamp: 1758233370 +I: Current time: Thu Oct 22 18:48:14 +14 2026 +I: pbuilder-time-stamp: 1792644494 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ dpkg-source: info: applying promod-executable.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/886740/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 22 04:48 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6b7da0c95e804347af6604500b044982' - 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='886740' - PS1='# ' - PS2='> ' + INVOCATION_ID=08d8bffcef3645ec981dc6890b8ba4c5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3517703 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.yYuuEnzw/pbuilderrc_cE7q --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1 --logfile b1/build.log promod3_3.4.2+ds-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/pbuilderrc_C3hE --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2 --logfile b2/build.log promod3_3.4.2+ds-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.12.43+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/886740/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -460,7 +492,7 @@ Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-2+b2 [2801 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.9.3-2 [3990 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.9.3-2 [93.1 MB] -Fetched 356 MB in 7s (52.1 MB/s) +Fetched 356 MB in 8s (43.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -1463,8 +1495,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Sep 18 22:14:40 UTC 2025. -Universal Time is now: Thu Sep 18 22:14:40 UTC 2025. +Local time is now: Thu Oct 22 04:53:29 UTC 2026. +Universal Time is now: Thu Oct 22 04:53:29 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-5) ... @@ -1722,7 +1754,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && 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 > ../promod3_3.4.2+ds-1_source.changes +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/promod3-3.4.2+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../promod3_3.4.2+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.2+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -5086,7 +5122,7 @@ Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 --- Configuring done (2.7s) +-- Configuring done (2.2s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -5103,7 +5139,7 @@ -- Build files have been written to: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds' dh_auto_build - cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -5112,151 +5148,157 @@ make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/depend make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/depend -make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" +make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/depend make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" +make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build +make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh +make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 +make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh -make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data +make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data +make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model +make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/sidechain/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build -make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py +make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/scoring/__init__.py +make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/loop/__init__.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build +make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/__init__.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.13/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data -[ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 0%] Generating ../stage/etc/bash_completion.d/pm-completion.bash make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake +[ 1%] Generating ../../stage/lib64/python3.13/site-packages/promod3/__init__.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 1%] Built target config_header -[ 1%] Built target loop_data_dir -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_closegaps.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.2 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend -[ 1%] Built target sidechain_data_dir -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" -[ 1%] Built target scoring_pymod +[ 1%] Built target loop_data_dir [ 1%] Built target sidechain_pymod -[ 1%] Built target loop_pymod -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/helper.py [ 1%] Built target scoring_data_dir -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_molprobity.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build -make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help +[ 1%] Built target loop_pymod +[ 1%] Built target config_header +[ 1%] Built target sidechain_data_dir +[ 1%] Built target scoring_pymod make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 1%] Built target subst_pm -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/tests make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend -[ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/core/pm3argparse.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/etc/bash_completion.d/pm-completion.bash -DPM3_ACTION_NAMES=build-model\ build-rawmodel\ help\ build-sidechains -P /build/reproducible-path/promod3-3.4.2+ds/cmake_support/substitute.cmake +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_pipeline.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains +[ 1%] Built target bash-completion +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build [ 1%] Built target init___init__.py_pymod +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend -[ 1%] Built target create_stage make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_ring_punches.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-help /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help -make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build +[ 1%] Built target create_stage +make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend +[ 1%] Built target core_pymod make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -5265,195 +5307,189 @@ cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_denovo.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm +[ 1%] Built target actions make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build -make[3]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. +make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/bin/pm +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build -make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build -make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build +make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh +make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build -[ 1%] Built target bash-completion -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh -[ 1%] Built target core_pymod -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_fragger_handle.py -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh [ 1%] Built target init_pymod +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py +[ 1%] Built target promod3_scripts cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py -[ 1%] Built target promod3_scripts -[ 1%] Built target actions -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_monte_carlo.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_raw_model.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_planar_rings.py +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh +[ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh -[ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +[ 1%] Built target promod3_core_headers +make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o +[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o +[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o +[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh +[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o +[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc +[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh -[ 1%] Built target promod3_core_headers -make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh +[ 5%] Built target promod3_modelling_headers cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh -[ 1%] Built target promod3_modelling_headers -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh -[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -[ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_base.cc +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/geom_stems.cc -[ 2%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/superpose.cc -[ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tree.cc -[ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/graph.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/tetrahedral_polytope.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/src/cluster.cc +[ 5%] Built target promod3_loop_headers cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.2+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_sidechain_headers make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_scoring_headers @@ -5475,38 +5511,38 @@ make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -[ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_runtime_profiling.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/backbone.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_graph_minimizer.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/core/pymod/export_geom.cc -[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -[ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -[ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o +[ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o +[ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o +[ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o cd 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loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/density_creator.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/frag_db.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF 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-std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/fragger.cc -[ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/forcefield_lookup.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/fragger.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_rule_lookup.cc -[ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/hydrogen_rule_lookup.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -MF CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o.d -o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o @@ -5637,60 +5673,74 @@ make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f 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-DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_amino_acid_atoms.cc +[ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_score_base.cc +[ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o +[ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc +[ 25%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o +[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc +[ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_positions.cc -[ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -[ 22%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB 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sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_overall_scorer.cc +[ 28%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/bb_dep_rotamer_lib.cc -[ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -[ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_backbone.cc -[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_forcefield_lookup.cc -[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/disulfid.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_score_base.cc -[ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_fragger.cc -[ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc -[ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_frag_db.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_loop_object_loader.cc +[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/frame.cc -[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o +[ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc +[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/backbone_overall_scorer.cc -[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o +[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_particle_scoring.cc -[ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o +[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl3_particle_scoring.cc -[ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/scoring_object_loader.cc -[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_particle_scoring.cc [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_mm_system_creator.cc -[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_env_listener.cc -[ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer.cc +[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc +[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_env_listener.cc +[ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_score.cc +[ 33%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc +[ 33%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc +[ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_particle_scoring.cc +[ 35%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -5727,38 +5777,52 @@ /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ -[ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/cb_packing_score.cc -[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o +[ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc +[ 36%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer.cc +[ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc +[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/density_score.cc +[ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc +[ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_density.cc -[ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o +[ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_group.cc -[ 33%] 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/build/reproducible-path/promod3-3.4.2+ds/scoring/src/cbeta_score.cc -[ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -[ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -[ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_psipred_prediction.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_structure_db.cc +[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_id.cc -[ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/reduced_env_listener.cc -[ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/export_torsion_sampler.cc -[ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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-DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_env_listener.cc -[ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o +[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c 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CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/clash_score.cc -[ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/density_score.cc -[ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o +[ 42%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong 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-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc +[ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc +[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc +[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc +[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc +[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc +[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc +[ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc +[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc +[ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/constraint_constructor.cc +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_overall_scorer.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -5777,55 +5841,27 @@ /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:32: note: '' declared here 66 | v.push_back(boost::python::extract(l[i])); | ^~~~~~~~~~~~~~~~ -[ 40%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_env_listener.cc -[ 42%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/loop/pymod/wrap_loop.cc -[ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/hbond_score.cc -[ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lib_reader.cc -[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_connector.cc -[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_score.cc -[ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/sidechain_object_loader.cc -[ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/ss_agreement_env_listener.cc -[ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/torsion_score.cc -[ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_constructor.cc -[ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/rotamer_lookup.cc -[ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o +[ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/scwrl4_rotamer_constructor.cc -[ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/pairwise_score.cc -[ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o +[ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc +[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc +[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK 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-DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_clash_score.cc +[ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o 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scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/constraint_constructor.cc -[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/vina_rotamer_constructor.cc -[ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o +[ 53%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/src/subrotamer_optimizer.cc -[ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_env_listener.cc -[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_interaction_score.cc -[ 52%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so +[ 53%] Linking CXX shared module ../../stage/lib64/python3.13/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_loop.dir/link.txt --verbose=1 -[ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_packing_score.cc /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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../../stage/lib64/libpromod3_loop.so.3.4.2 /usr/lib/x86_64-linux-gnu/libpython3.13.so /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 52%] Built target _loop -[ 53%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/src/all_atom_clash_score.cc +[ 53%] Built target _loop [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_scoring.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/promod3_scoring.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libpromod3_scoring.so.3.4 -o ../../stage/lib64/libpromod3_scoring.so.3.4.2 CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o CMakeFiles/promod3_scoring.dir/clash_score.cc.o CMakeFiles/promod3_scoring.dir/density_score.cc.o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -L/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.2 ../../stage/lib64/libpromod3_core.so.3.4.2 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -5838,21 +5874,21 @@ make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -[ 56%] Building CXX object 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-I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_density_scorer.cc -[ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o +[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o +[ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o +[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc +[ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o +[ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o +[ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_pairwise_functions.cc +[ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o +[ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_density_scorer.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK 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Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/promod3_sidechain.dir/link.txt --verbose=1 @@ -5863,43 +5899,53 @@ make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod 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sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c 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-I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/extension_scheme.cc -[ 63%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_connector.cc +[ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o +[ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o +[ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c 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CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_frame.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_graph.cc [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_particle.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -[ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/gap_extender.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer.cc -[ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_cruncher.cc -[ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/backbone_relaxer.cc +[ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_density.cc +[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc +[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -5926,30 +5972,32 @@ /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o +[ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_rotamer_ids.cc -[ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/ccd.cc -[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/kic.cc -[ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o +[ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong 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-D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_sidechain_object_loader.cc -[ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/loop_candidate.cc -[ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o +[ 74%] Building CXX object 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modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo.cc -[ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o +[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. 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-I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc +[ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc +[ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/export_subrotamer_optimizer.cc -[ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_closer.cc -[ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o +[ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/sidechain/pymod/wrap_sidechain.cc -[ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_cooler.cc +[ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/rigid_blocks.cc +[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc +[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/scoring_weights.cc +[ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_reconstructor.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -5986,6 +6034,8 @@ /build/reproducible-path/promod3-3.4.2+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ +[ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/sidechain_env_listener.cc 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, @@ -5998,20 +6048,6 @@ /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_sampler.cc -[ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/monte_carlo_scorer.cc -[ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/rigid_blocks.cc -[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/src/score_container.cc -[ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c 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-DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -MF CMakeFiles/_modelling.dir/export_scoring_weights.cc.o.d -o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o +[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_afdb.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_loop_closure.cc +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -MF CMakeFiles/_modelling.dir/export_monte_carlo.cc.o.d -o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_monte_carlo.cc [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -[ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_sidechain_reconstructor.cc +[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o -MF CMakeFiles/_modelling.dir/export_gap.cc.o.d -o CMakeFiles/_modelling.dir/export_gap.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_gap.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -MF CMakeFiles/_modelling.dir/export_motif_finder.cc.o.d -o CMakeFiles/_modelling.dir/export_motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_motif_finder.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_rigid_blocks.cc +[ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_sidechain_reconstructor.cc -[ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_afdb.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -6109,7 +6147,7 @@ from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:17: + from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, @@ -6117,7 +6155,7 @@ /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ -In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:19: +In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); @@ -6135,7 +6173,7 @@ from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:17: + from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:17: 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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:1176:20, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/15/bits/basic_string.h:617:20, @@ -6143,13 +6181,11 @@ /usr/include/c++/15/bits/basic_string.h:1165:19: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)& + offsetof(boost::python::extract, std::allocator > >,boost::python::extract, std::allocator > >::.boost::python::converter::extract_rvalue, std::allocator > >::m_data.boost::python::converter::rvalue_from_python_data, std::allocator > >::.boost::python::converter::rvalue_from_python_storage, std::allocator > >::storage)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1165 | size_type __sz = _M_string_length; | ^~~~ -In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_score_container.cc:19: +In file included from /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/export_scoring_weights.cc:19: /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh: In function 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]': /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:83:34: note: '' declared here 83 | const K key = boost::python::extract(keys[i]); | ^~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.13 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.2+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.2+ds/modelling/pymod/wrap_modelling.cc In file included from /usr/include/c++/15/string:56, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, @@ -6227,98 +6263,134 @@ make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/depend make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/depend -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend -make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend +make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" -make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" +make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data 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sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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+make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu 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'/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build -make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build +make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build -make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build +make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat -[ 91%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat -[ 98%] Generating ../../stage/share/promod3/loop_data/structure_db.dat -[ 97%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat -[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat -[ 98%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat -[ 91%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat -[ 91%] Generating ../../stage/share/promod3/loop_data/frag_db.dat +[ 90%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat +[ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler +[ 94%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 94%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat +[ 95%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup +[ 95%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat +[ 97%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat +[ 97%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat +[ 97%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer +[ 97%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer +[ 97%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat +[ 98%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer +[ 98%] Generating ../../stage/share/promod3/loop_data/frag_db.dat +[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer +cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. +Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. @@ -6367,98 +6439,54 @@ pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/promod3/modelling/_afdb_modelling.py:633: SyntaxWarning: invalid escape sequence '\.' - pat = f"ling {cname}\.[A-Z]+([0-9]*)-\([A-Z]+\)-{cname}\.[A-Z]+([0-9]+)" -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 98%] Built target generate_scoring_data_cbeta_scorer.dat -[ 98%] Built target generate_scoring_data_cb_packing_scorer.dat -[ 98%] Built target generate_scoring_data_hbond_scorer.dat -make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/depend -make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/depend -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" -[ 98%] Built target generate_loop_data_ff_lookup_charmm.dat -[ 98%] Built target generate_scoring_data_aa_packing_scorer.dat -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend +[100%] Built target generate_scoring_data_cbeta_scorer.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake "--color=" +[100%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build +[100%] Built target generate_scoring_data_cb_packing_scorer.dat +[100%] Built target generate_scoring_data_hbond_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build -make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[ 98%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat -[ 98%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.2+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer -[100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat -cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib +[100%] Built target generate_scoring_data_ss_agreement_scorer.dat +[100%] Built target generate_scoring_data_aa_scorer.dat [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat +[100%] Built target generate_loop_data_ff_lookup_charmm.dat cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/lib64/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.2+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. -Compound library not available. Some functionality may not work as expected. -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_ss_agreement_scorer.dat -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat -[100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +Compound library not available. Some functionality may not work as expected. [100%] Built target generate_scoring_data_reduced_scorer.dat -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' -[100%] Built target generate_loop_data_torsion_sampler_helical.dat -[100%] Built target generate_loop_data_torsion_sampler_extended.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_loop_data_torsion_sampler_extended.dat +[100%] Built target generate_loop_data_torsion_sampler_helical.dat +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_coil.dat -[100%] Built target generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_loop_data_torsion_sampler.dat [100%] Built target generate_sidechain_data_bb_dep_lib.dat +make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' +[100%] Built target generate_sidechain_data_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.2+ds /build/reproducible-path/promod3-3.4.2+ds/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" @@ -6718,7 +6746,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.094s +Ran 2 tests in 0.127s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -6734,7 +6762,7 @@ Compound library not available. Some functionality may not work as expected. ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.001s +Ran 12 tests in 0.002s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -6750,7 +6778,7 @@ Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- -Ran 66 tests in 1.198s +Ran 66 tests in 1.535s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7586,7 +7614,7 @@ Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- -Ran 33 tests in 18.121s +Ran 33 tests in 18.709s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7602,7 +7630,7 @@ Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.013s +Ran 6 tests in 0.017s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7621,7 +7649,7 @@ residue A.GLY8 is missing atoms CA ........ ---------------------------------------------------------------------- -Ran 25 tests in 0.068s +Ran 25 tests in 0.103s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7638,7 +7666,7 @@ Switched to slower reference platform of OpenMM! ............... ---------------------------------------------------------------------- -Ran 15 tests in 28.434s +Ran 15 tests in 30.975s OK OpenMM CPU platform not available. Skipping almost_on_top check. @@ -7656,7 +7684,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.078s +Ran 2 tests in 0.108s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7672,7 +7700,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 1.618s +Ran 2 tests in 2.034s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7688,7 +7716,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.009s +Ran 2 tests in 0.010s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7723,7 +7751,7 @@ Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- -Ran 3 tests in 4.016s +Ran 3 tests in 5.328s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7739,7 +7767,7 @@ Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- -Ran 3 tests in 1.059s +Ran 3 tests in 1.670s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7755,7 +7783,7 @@ Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- -Ran 2 tests in 0.025s +Ran 2 tests in 0.036s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' @@ -7786,7 +7814,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/reproducible-path/promod3-3.4.2\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.2+ds -B/build/reproducible-path/promod3-3.4.2+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -8011,9 +8039,9 @@ dh_installchangelogs dh_python3 I: dh_python3 fs:421: renaming _modelling.so to _modelling.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _loop.so to _loop.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming _scoring.so to _scoring.cpython-313-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming _core.so to _core.cpython-313-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.cpython-313-x86_64-linux-gnu.so dh_perl dh_link @@ -8032,16 +8060,16 @@ dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.2+ds-1_all.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.2+ds-1_amd64.deb'. -dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.2+ds-1_amd64.deb'. +dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.2+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.2+ds-1_amd64.deb'. @@ -8056,12 +8084,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3517703/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/886740 and its subdirectories -I: Current time: Thu Sep 18 10:25:00 -12 2025 -I: pbuilder-time-stamp: 1758234300 +I: removing directory /srv/workspace/pbuilder/3517703 and its subdirectories +I: Current time: Thu Oct 22 19:02:58 +14 2026 +I: pbuilder-time-stamp: 1792645378 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/promod3_3.4.2+ds-1.diff: 95.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/promod3_3.4.2+ds-1.diff.gz b2/build.log: 93.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 94.0% -- replaced with stdout Thu Sep 18 22:40:07 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_promod3_unstable_amd64_1758235207 + touch /var/log/reproducible-builds/diffoscope_stamp_promod3_unstable_amd64_1758235207 + RESULT=0 + systemd-run '--description=diffoscope on promod3/3.4.2+ds-1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_35-78648 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw --run-session -c jenkins-reproducible-unstable-diffoscope-5f8b3172-dc65-4f0e-9449-457593731904 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/dbd-tmp-p7ss9DK ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1/promod3_3.4.2+ds-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2/promod3_3.4.2+ds-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_35-78648.service; invocation ID: b30b1af117d14e14bda6fa4a8d60da26 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/promod3_3.4.2+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b1/promod3_3.4.2+ds-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yYuuEnzw/b2/promod3_3.4.2+ds-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 201ms CPU time consumed: 171ms Memory peak: 17.4M (swap: 0B) _ _____ _ __ _ __ ___ _ __ ___ ___ __| |___ / | '_ \| '__/ _ \| '_ ` _ \ / _ \ / _` | |_ \ | |_) | | | (_) | | | | | | (_) | (_| |___) | | .__/|_| \___/|_| |_| |_|\___/ \__,_|____/ |_| Thu Sep 18 22:40:13 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 22:40:13 UTC 2025 I: promod3 from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 22:40:14] INFO: Starting at 2025-09-18 22:40:14.039340 [2025-09-18 22:40:14] INFO: Generating the pages of 1 package(s) [2025-09-18 22:40:14] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/promod3 didn't produce a buildlog, even though it has been built. [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/promod3_3.2.1+ds-6.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/promod3_3.2.1+ds-6.diff.gz is missing [2025-09-18 22:40:14] INFO: Finished at 2025-09-18 22:40:14.362156, took: 0:00:00.322820 Thu Sep 18 22:40:14 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/promod3.html Thu Sep 18 22:40:14 UTC 2025 I: Removing signed promod3_3.4.2+ds-1_amd64.buildinfo.asc files: removed './b1/promod3_3.4.2+ds-1_amd64.buildinfo.asc' removed './b2/promod3_3.4.2+ds-1_amd64.buildinfo.asc' 1758235214 amd64 unstable promod3 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/promod3_3.4.2+ds-1.rbuild.log: 93.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/promod3_3.4.2+ds-1.rbuild.log.gz [2025-09-18 22:40:14] INFO: Starting at 2025-09-18 22:40:14.719912 [2025-09-18 22:40:14] INFO: Generating the pages of 1 package(s) [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/forky/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:14] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/promod3_3.4.2+ds-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/promod3_3.4.2+ds-1.diff.gz is missing [2025-09-18 22:40:15] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/arm64/promod3_3.2.1+ds-6.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/arm64/promod3_3.2.1+ds-6.diff.gz is missing [2025-09-18 22:40:15] INFO: Finished at 2025-09-18 22:40:15.013009, took: 0:00:00.293099 All cleanup done. Thu Sep 18 22:40:15 UTC 2025 - total duration: 0h 31m 0s. Thu Sep 18 22:40:15 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-3bhnVcBr, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 31min 2.371s CPU time consumed: 13.946s Memory peak: 1.6G (swap: 0B)