Tue Oct 21 20:09:43 UTC 2025 I: starting to build promod3/forky/amd64 on jenkins on '2025-10-21 20:09' Tue Oct 21 20:09:43 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_20/70952/console.log Tue Oct 21 20:09:43 UTC 2025 I: Downloading source for forky/promod3=3.6.0+ds-1 --2025-10-21 20:09:43-- http://deb.debian.org/debian/pool/main/p/promod3/promod3_3.6.0%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3239 (3.2K) [text/prs.lines.tag] Saving to: ‘promod3_3.6.0+ds-1.dsc’ 0K ... 100% 347M=0s 2025-10-21 20:09:43 (347 MB/s) - ‘promod3_3.6.0+ds-1.dsc’ saved [3239/3239] Tue Oct 21 20:09:43 UTC 2025 I: promod3_3.6.0+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: promod3 Binary: libpromod3-core-dev, libpromod3-core3.6, libpromod3-loop-dev, libpromod3-loop3.6, libpromod3-modelling-dev, libpromod3-modelling3.6, libpromod3-scoring-dev, libpromod3-scoring3.6, libpromod3-sidechain-dev, libpromod3-sidechain3.6, promod3, promod3-data, python3-promod3 Architecture: any all Version: 3.6.0+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-core3.6 deb libs optional arch=any libpromod3-loop-dev deb libdevel optional arch=any libpromod3-loop3.6 deb libs optional arch=any libpromod3-modelling-dev deb libdevel optional arch=any libpromod3-modelling3.6 deb libs optional arch=any libpromod3-scoring-dev deb libdevel optional arch=any libpromod3-scoring3.6 deb libs optional arch=any libpromod3-sidechain-dev deb libdevel optional arch=any libpromod3-sidechain3.6 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: 184982d8a918a4b4685f014929d3adf9aadbc8b3 398645964 promod3_3.6.0+ds.orig.tar.xz da3681490668989171693b1cb0a29933686a3591 5908 promod3_3.6.0+ds-1.debian.tar.xz Checksums-Sha256: 6be0d71a0418384f1119a7af276edacd0ea861bcbcde41ce1a251d11a6b90435 398645964 promod3_3.6.0+ds.orig.tar.xz 9d78900f0ab657aa336a8f680eb38e79ac4d9b7be9ed1d8a07e855df966d1aab 5908 promod3_3.6.0+ds-1.debian.tar.xz Files: 9859bcbeaa3e08eb28c2b737363be616 398645964 promod3_3.6.0+ds.orig.tar.xz cd9f8a0f542914da69465ee3606b590b 5908 promod3_3.6.0+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmjwmucSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHJvYP/RYmtpJsGIbUeh1jL+zxPtIuIrrPIzzf 3H10N6NaIs9hp9C/awaaKVbf10ZE2vm2q4LxkHGy+WIzKX6VaOOcE9LnPVQEFk1L QovvqXZA7IbzXvujjAAiyENGONuZjbIW/tC9bPfqVtmNbIIsAYlDzmULKCVg87Ym cJ4ZJikqoKVccnTsjX/uhW5sm7E0qZXvpQKKPmjn/YehiHWyIWnXdUczu2z56M28 7zRznDvcjCJt2xG9dpStV0Zt9/+Vg1/e9WGKWF2p0BylbiRCS2qHa2wYWmrBVrnP v8eE5dynd7vvYiJJ3J8wur5QMicB0zJvivLwONGwoFy5V2vhwLhZkX7zv7k9Y9zT OsQtwxNqKjLCIlWbt/OTXQ66d2FzhbfEGn8sn7ShfW7V13SlSS4YYhK1Hh6Ih8Xa W5+HP1OMexmDnUqnp4P6HewcUkqZqV7VABOmeHYQJZELDGJ8dPmaF167Mude3zUE GtLmedXBTDiw7JDQQ3T5lrcwt49k/m0cWmtKxtWqPSAtav+JWV9IAsKLeC4YFxxb /ctii8Jz1O8AszB/tCNuMxoysJW80xzNgfWHkpXG4S9xbnsckXfMxdGq25cX5mnE bzsSbs6meGbIJ8G7807bCO9MLk2xah79lCGdU6qptG/RyB5Iu8Je5kN4ifeqi7NT bzYzpLv2aBMz =6WpJ -----END PGP SIGNATURE----- Tue Oct 21 20:09:43 UTC 2025 I: Checking whether the package is not for us Tue Oct 21 20:09:43 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Oct 21 20:09:43 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Oct 21 20:23:03 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 23 14:32:49 -12 2026 I: pbuilder-time-stamp: 1795487569 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_3.6.0+ds-1.dsc] I: copying [./promod3_3.6.0+ds.orig.tar.xz] I: copying [./promod3_3.6.0+ds-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./promod3_3.6.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.6.0+ds dpkg-source: info: unpacking promod3_3.6.0+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.6.0+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/1521066/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=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='67b350dea3764d0084039f42c1366414' 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='1521066' 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.2ngCPHIK/pbuilderrc_cfCo --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/b1 --logfile b1/build.log promod3_3.6.0+ds-1.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) 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/1521066/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 ... 19898 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} libngtcp2-16{a} libngtcp2-crypto-ossl0{a} libopengl0{a} libopenjp2-7{a} libopenmm8.1{a} libost-base-dev{a} libost-base2.11{a} libost-bindings2.11{a} libost-conop-dev{a} libost-conop2.11{a} libost-db2.11{a} libost-geom-dev{a} libost-geom2.11{a} libost-gfx2.11{a} libost-gui2.11{a} libost-img-alg2.11{a} libost-img-dev{a} libost-img2.11{a} libost-info-dev{a} libost-info2.11{a} libost-io-dev{a} libost-io2.11{a} libost-mol-alg-dev{a} libost-mol-alg2.11{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.11{a} libost-mol2.11{a} libost-seq-alg-dev{a} libost-seq-alg2.11{a} libost-seq-dev{a} libost-seq2.11{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} librav1e0.8{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, 309 newly installed, 0 to remove and 0 not upgraded. Need to get 356 MB of archives. After unpacking 1324 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.9-1 [865 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.9-1 [2257 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.9-1 [1965 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.9-1 [764 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libtcl8.6 amd64 8.6.17+dfsg-1 [1041 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libpng16-16t64 amd64 1.6.50-1 [282 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 fontconfig-config amd64 2.15.0-2.4 [318 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libfontconfig1 amd64 2.15.0-2.4 [401 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 x11-common all 1:7.7+25 [217 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libtk8.6 amd64 8.6.17-1 [794 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-8 [591 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 blt amd64 2.5.3+dfsg-8 [5984 B] Get: 58 http://deb.debian.org/debian forky/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 67 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 78 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.16.0-4 [408 kB] Get: 83 http://deb.debian.org/debian forky/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 86 http://deb.debian.org/debian forky/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 87 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 90 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 92 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 93 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 dh-python all 6.20250414 [116 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 fontconfig amd64 2.15.0-2.4 [464 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 fonts-lyx all 2.4.4-2 [190 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 103 http://deb.debian.org/debian forky/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get: 104 http://deb.debian.org/debian forky/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get: 105 http://deb.debian.org/debian forky/main amd64 libabsl20240722 amd64 20240722.0-4 [492 kB] Get: 106 http://deb.debian.org/debian forky/main amd64 libaom3 amd64 3.13.1-1 [1905 kB] Get: 107 http://deb.debian.org/debian forky/main amd64 libavahi-common-data amd64 0.8-17 [112 kB] Get: 108 http://deb.debian.org/debian forky/main amd64 libavahi-common3 amd64 0.8-17 [47.3 kB] Get: 109 http://deb.debian.org/debian forky/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB] Get: 110 http://deb.debian.org/debian forky/main amd64 libavahi-client3 amd64 0.8-17 [52.1 kB] Get: 111 http://deb.debian.org/debian forky/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB] Get: 112 http://deb.debian.org/debian forky/main amd64 libgav1-1 amd64 0.19.0-3+b1 [353 kB] Get: 113 http://deb.debian.org/debian forky/main amd64 librav1e0.8 amd64 0.8.1-5 [976 kB] Get: 114 http://deb.debian.org/debian forky/main amd64 libsvtav1enc2 amd64 2.3.0+dfsg-1 [2489 kB] Get: 115 http://deb.debian.org/debian forky/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 116 http://deb.debian.org/debian forky/main amd64 libyuv0 amd64 0.0.1919.20250919-1 [175 kB] Get: 117 http://deb.debian.org/debian forky/main amd64 libavif16 amd64 1.3.0-1+b1 [137 kB] Get: 118 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 119 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 120 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 121 http://deb.debian.org/debian forky/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get: 122 http://deb.debian.org/debian forky/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get: 123 http://deb.debian.org/debian forky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get: 124 http://deb.debian.org/debian forky/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get: 125 http://deb.debian.org/debian forky/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get: 126 http://deb.debian.org/debian forky/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get: 127 http://deb.debian.org/debian forky/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 128 http://deb.debian.org/debian forky/main amd64 libboost-regex1.83.0 amd64 1.83.0-5 [336 kB] Get: 129 http://deb.debian.org/debian forky/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get: 130 http://deb.debian.org/debian forky/main amd64 libboost-regex1.83-dev amd64 1.83.0-5 [352 kB] Get: 131 http://deb.debian.org/debian forky/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-5 [265 kB] Get: 132 http://deb.debian.org/debian forky/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 133 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get: 134 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83-dev amd64 1.83.0-5 [385 kB] Get: 135 http://deb.debian.org/debian forky/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 136 http://deb.debian.org/debian forky/main amd64 libboost-python1.83.0 amd64 1.83.0-5 [313 kB] Get: 137 http://deb.debian.org/debian forky/main amd64 libpython3.13 amd64 3.13.9-1 [2184 kB] Get: 138 http://deb.debian.org/debian forky/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Get: 139 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 140 http://deb.debian.org/debian forky/main amd64 libpython3.13-dev amd64 3.13.9-1 [5311 kB] Get: 141 http://deb.debian.org/debian forky/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 142 http://deb.debian.org/debian forky/main amd64 python3.13-dev amd64 3.13.9-1 [504 kB] Get: 143 http://deb.debian.org/debian forky/main amd64 libjs-sphinxdoc all 8.2.3-7 [27.6 kB] Get: 144 http://deb.debian.org/debian forky/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 145 http://deb.debian.org/debian forky/main amd64 libboost-python1.83-dev amd64 1.83.0-5 [337 kB] Get: 146 http://deb.debian.org/debian forky/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 147 http://deb.debian.org/debian forky/main amd64 libboost-test1.83.0 amd64 1.83.0-5 [488 kB] Get: 148 http://deb.debian.org/debian forky/main amd64 libboost-test1.83-dev amd64 1.83.0-5 [560 kB] Get: 149 http://deb.debian.org/debian forky/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 150 http://deb.debian.org/debian forky/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get: 151 http://deb.debian.org/debian forky/main amd64 libcups2t64 amd64 2.4.14-1 [255 kB] Get: 152 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 153 http://deb.debian.org/debian forky/main amd64 libdouble-conversion3 amd64 3.3.1-2 [41.5 kB] Get: 154 http://deb.debian.org/debian forky/main amd64 libdrm-common all 2.4.125-2 [8576 B] Get: 155 http://deb.debian.org/debian forky/main amd64 libdrm2 amd64 2.4.125-2 [39.1 kB] Get: 156 http://deb.debian.org/debian forky/main amd64 libdrm-amdgpu1 amd64 2.4.125-2 [23.2 kB] Get: 157 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get: 158 http://deb.debian.org/debian forky/main amd64 libdrm-intel1 amd64 2.4.125-2 [64.1 kB] Get: 159 http://deb.debian.org/debian forky/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get: 160 http://deb.debian.org/debian forky/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 161 http://deb.debian.org/debian forky/main amd64 libllvm19 amd64 1:19.1.7-7 [25.9 MB] Get: 162 http://deb.debian.org/debian forky/main amd64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get: 163 http://deb.debian.org/debian forky/main amd64 libsensors5 amd64 1:3.6.2-2 [37.5 kB] Get: 164 http://deb.debian.org/debian forky/main amd64 libx11-xcb1 amd64 2:1.8.12-1 [247 kB] Get: 165 http://deb.debian.org/debian forky/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 166 http://deb.debian.org/debian forky/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 167 http://deb.debian.org/debian forky/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 168 http://deb.debian.org/debian forky/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 169 http://deb.debian.org/debian forky/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 170 http://deb.debian.org/debian forky/main amd64 libxshmfence1 amd64 1.3.3-1 [10.9 kB] Get: 171 http://deb.debian.org/debian forky/main amd64 mesa-libgallium amd64 25.2.5-1 [10.3 MB] Get: 172 http://deb.debian.org/debian forky/main amd64 libgbm1 amd64 25.2.5-1 [46.0 kB] Get: 173 http://deb.debian.org/debian forky/main amd64 libwayland-client0 amd64 1.24.0-2+b1 [28.5 kB] Get: 174 http://deb.debian.org/debian forky/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 175 http://deb.debian.org/debian forky/main amd64 libegl-mesa0 amd64 25.2.5-1 [123 kB] Get: 176 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 177 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 178 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 179 http://deb.debian.org/debian forky/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 180 http://deb.debian.org/debian forky/main amd64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 181 http://deb.debian.org/debian forky/main amd64 libevdev2 amd64 1.13.4+dfsg-1 [32.4 kB] Get: 182 http://deb.debian.org/debian forky/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 183 http://deb.debian.org/debian forky/main amd64 libfribidi0 amd64 1.0.16-3 [26.6 kB] Get: 184 http://deb.debian.org/debian forky/main amd64 libgpg-error0 amd64 1.56-2 [89.1 kB] Get: 185 http://deb.debian.org/debian forky/main amd64 libgcrypt20 amd64 1.11.2-2 [865 kB] Get: 186 http://deb.debian.org/debian forky/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 187 http://deb.debian.org/debian forky/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 188 http://deb.debian.org/debian forky/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b4 [19.3 kB] Get: 189 http://deb.debian.org/debian forky/main amd64 libvulkan1 amd64 1.4.321.0-1 [133 kB] Get: 190 http://deb.debian.org/debian forky/main amd64 libgl1-mesa-dri amd64 25.2.5-1 [47.8 kB] Get: 191 http://deb.debian.org/debian forky/main amd64 libglx-mesa0 amd64 25.2.5-1 [116 kB] Get: 192 http://deb.debian.org/debian forky/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 193 http://deb.debian.org/debian forky/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 194 http://deb.debian.org/debian forky/main amd64 libglib2.0-0t64 amd64 2.86.0-5 [1544 kB] Get: 195 http://deb.debian.org/debian forky/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 196 http://deb.debian.org/debian forky/main amd64 libglu1-mesa amd64 9.0.2-1.1+b3 [184 kB] Get: 197 http://deb.debian.org/debian forky/main amd64 libgraphite2-3 amd64 1.3.14-11 [76.7 kB] Get: 198 http://deb.debian.org/debian forky/main amd64 libgudev-1.0-0 amd64 238-7 [14.6 kB] Get: 199 http://deb.debian.org/debian forky/main amd64 libharfbuzz0b amd64 12.1.0-1 [530 kB] Get: 200 http://deb.debian.org/debian forky/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 201 http://deb.debian.org/debian forky/main amd64 libimagequant0 amd64 4.4.0-3 [251 kB] Get: 202 http://deb.debian.org/debian forky/main amd64 libwacom-common all 2.16.1-1 [112 kB] Get: 203 http://deb.debian.org/debian forky/main amd64 libwacom9 amd64 2.16.1-1 [26.8 kB] Get: 204 http://deb.debian.org/debian forky/main amd64 libinput-bin amd64 1.28.1-1 [26.3 kB] Get: 205 http://deb.debian.org/debian forky/main amd64 libmtdev1t64 amd64 1.1.7-1 [22.6 kB] Get: 206 http://deb.debian.org/debian forky/main amd64 libinput10 amd64 1.28.1-1 [143 kB] Get: 207 http://deb.debian.org/debian forky/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 208 http://deb.debian.org/debian forky/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 209 http://deb.debian.org/debian forky/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 210 http://deb.debian.org/debian forky/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get: 211 http://deb.debian.org/debian forky/main amd64 libopenjp2-7 amd64 2.5.3-2.1 [204 kB] Get: 212 http://deb.debian.org/debian forky/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-12 [1052 kB] Get: 213 http://deb.debian.org/debian forky/main amd64 libost-base2.11 amd64 2.11.1-1 [36.3 kB] Get: 214 http://deb.debian.org/debian forky/main amd64 libost-base-dev amd64 2.11.1-1 [30.0 kB] Get: 215 http://deb.debian.org/debian forky/main amd64 libost-geom2.11 amd64 2.11.1-1 [67.5 kB] Get: 216 http://deb.debian.org/debian forky/main amd64 libost-mol2.11 amd64 2.11.1-1 [403 kB] Get: 217 http://deb.debian.org/debian forky/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get: 218 http://deb.debian.org/debian forky/main amd64 libpcre2-16-0 amd64 10.46-1 [281 kB] Get: 219 http://deb.debian.org/debian forky/main amd64 libqt5core5t64 amd64 5.15.17+dfsg-4 [1898 kB] Get: 220 http://deb.debian.org/debian forky/main amd64 libqt5xml5t64 amd64 5.15.17+dfsg-4 [127 kB] Get: 221 http://deb.debian.org/debian forky/main amd64 libost-info2.11 amd64 2.11.1-1 [171 kB] Get: 222 http://deb.debian.org/debian forky/main amd64 libost-seq2.11 amd64 2.11.1-1 [92.4 kB] Get: 223 http://deb.debian.org/debian forky/main amd64 libost-bindings2.11 amd64 2.11.1-1 [206 kB] Get: 224 http://deb.debian.org/debian forky/main amd64 libost-conop2.11 amd64 2.11.1-1 [192 kB] Get: 225 http://deb.debian.org/debian forky/main amd64 libost-conop-dev amd64 2.11.1-1 [24.4 kB] Get: 226 http://deb.debian.org/debian forky/main amd64 libost-db2.11 amd64 2.11.1-1 [46.2 kB] Get: 227 http://deb.debian.org/debian forky/main amd64 libost-geom-dev amd64 2.11.1-1 [31.0 kB] Get: 228 http://deb.debian.org/debian forky/main amd64 libost-img2.11 amd64 2.11.1-1 [145 kB] Get: 229 http://deb.debian.org/debian forky/main amd64 libost-img-alg2.11 amd64 2.11.1-1 [171 kB] Get: 230 http://deb.debian.org/debian forky/main amd64 libost-gfx2.11 amd64 2.11.1-1 [438 kB] Get: 231 http://deb.debian.org/debian forky/main amd64 libost-mol-alg2.11 amd64 2.11.1-1 [376 kB] Get: 232 http://deb.debian.org/debian forky/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 233 http://deb.debian.org/debian forky/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 234 http://deb.debian.org/debian forky/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get: 235 http://deb.debian.org/debian forky/main amd64 libost-io2.11 amd64 2.11.1-1 [927 kB] Get: 236 http://deb.debian.org/debian forky/main amd64 libparasail8 amd64 2.6.2+dfsg-2 [1890 kB] Get: 237 http://deb.debian.org/debian forky/main amd64 libost-seq-alg2.11 amd64 2.11.1-1 [256 kB] Get: 238 http://deb.debian.org/debian forky/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 239 http://deb.debian.org/debian forky/main amd64 libqt5dbus5t64 amd64 5.15.17+dfsg-4 [219 kB] Get: 240 http://deb.debian.org/debian forky/main amd64 libqt5network5t64 amd64 5.15.17+dfsg-4 [692 kB] Get: 241 http://deb.debian.org/debian forky/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB] Get: 242 http://deb.debian.org/debian forky/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get: 243 http://deb.debian.org/debian forky/main amd64 libxcb-util1 amd64 0.4.1-1 [23.5 kB] Get: 244 http://deb.debian.org/debian forky/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get: 245 http://deb.debian.org/debian forky/main amd64 libxcb-keysyms1 amd64 0.4.1-1 [16.7 kB] Get: 246 http://deb.debian.org/debian forky/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 247 http://deb.debian.org/debian forky/main amd64 libxcb-render-util0 amd64 0.3.10-1 [18.4 kB] Get: 248 http://deb.debian.org/debian forky/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get: 249 http://deb.debian.org/debian forky/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get: 250 http://deb.debian.org/debian forky/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get: 251 http://deb.debian.org/debian forky/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get: 252 http://deb.debian.org/debian forky/main amd64 xkb-data all 2.42-1 [790 kB] Get: 253 http://deb.debian.org/debian forky/main amd64 libxkbcommon0 amd64 1.7.0-2.1 [113 kB] Get: 254 http://deb.debian.org/debian forky/main amd64 libxkbcommon-x11-0 amd64 1.7.0-2.1 [16.2 kB] Get: 255 http://deb.debian.org/debian forky/main amd64 libqt5gui5t64 amd64 5.15.17+dfsg-4 [3534 kB] Get: 256 http://deb.debian.org/debian forky/main amd64 libqt5widgets5t64 amd64 5.15.17+dfsg-4 [2424 kB] Get: 257 http://deb.debian.org/debian forky/main amd64 libost-gui2.11 amd64 2.11.1-1 [513 kB] Get: 258 http://deb.debian.org/debian forky/main amd64 libost-img-dev amd64 2.11.1-1 [45.5 kB] Get: 259 http://deb.debian.org/debian forky/main amd64 libost-info-dev amd64 2.11.1-1 [22.8 kB] Get: 260 http://deb.debian.org/debian forky/main amd64 libost-io-dev amd64 2.11.1-1 [54.8 kB] Get: 261 http://deb.debian.org/debian forky/main amd64 libost-mol-alg-dev amd64 2.11.1-1 [33.6 kB] Get: 262 http://deb.debian.org/debian forky/main amd64 libost-mol-dev amd64 2.11.1-1 [60.3 kB] Get: 263 http://deb.debian.org/debian forky/main amd64 libost-mol-mm2.11 amd64 2.11.1-1 [294 kB] Get: 264 http://deb.debian.org/debian forky/main amd64 libost-mol-mm-dev amd64 2.11.1-1 [30.7 kB] Get: 265 http://deb.debian.org/debian forky/main amd64 libost-seq-alg-dev amd64 2.11.1-1 [181 kB] Get: 266 http://deb.debian.org/debian forky/main amd64 libost-seq-dev amd64 2.11.1-1 [26.9 kB] Get: 267 http://deb.debian.org/debian forky/main amd64 libqhull-r8.0 amd64 2020.2-7 [248 kB] Get: 268 http://deb.debian.org/debian forky/main amd64 libqt5designer5 amd64 5.15.17-3 [2760 kB] Get: 269 http://deb.debian.org/debian forky/main amd64 libqt5sql5t64 amd64 5.15.17+dfsg-4 [126 kB] Get: 270 http://deb.debian.org/debian forky/main amd64 libqt5help5 amd64 5.15.17-3 [150 kB] Get: 271 http://deb.debian.org/debian forky/main amd64 libqt5printsupport5t64 amd64 5.15.17+dfsg-4 [208 kB] Get: 272 http://deb.debian.org/debian forky/main amd64 libqt5test5t64 amd64 5.15.17+dfsg-4 [153 kB] Get: 273 http://deb.debian.org/debian forky/main amd64 libraqm0 amd64 0.10.3-1 [14.0 kB] Get: 274 http://deb.debian.org/debian forky/main amd64 libsqlite3-dev amd64 3.46.1-8 [1172 kB] Get: 275 http://deb.debian.org/debian forky/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 276 http://deb.debian.org/debian forky/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 277 http://deb.debian.org/debian forky/main amd64 libxslt1.1 amd64 1.1.43-0.2 [155 kB] Get: 278 http://deb.debian.org/debian forky/main amd64 libzopfli1 amd64 1.0.3-3 [106 kB] Get: 279 http://deb.debian.org/debian forky/main amd64 python-matplotlib-data all 3.10.1+dfsg1-6 [2737 kB] Get: 280 http://deb.debian.org/debian forky/main amd64 python3-dateutil all 2.9.0-4 [79.4 kB] Get: 281 http://deb.debian.org/debian forky/main amd64 python3-pil amd64 11.3.0-1 [526 kB] Get: 282 http://deb.debian.org/debian forky/main amd64 python3.13-tk amd64 3.13.9-1 [108 kB] Get: 283 http://deb.debian.org/debian forky/main amd64 python3-tk amd64 3.13.5-1 [9604 B] Get: 284 http://deb.debian.org/debian forky/main amd64 python3-pil.imagetk amd64 11.3.0-1 [81.1 kB] Get: 285 http://deb.debian.org/debian forky/main amd64 python3-pyparsing all 3.1.3-1 [148 kB] Get: 286 http://deb.debian.org/debian forky/main amd64 python3-contourpy amd64 1.3.1-2 [215 kB] Get: 287 http://deb.debian.org/debian forky/main amd64 python3-cycler all 0.12.1-2 [9616 B] Get: 288 http://deb.debian.org/debian forky/main amd64 python3-brotli amd64 1.1.0-2+b7 [320 kB] Get: 289 http://deb.debian.org/debian forky/main amd64 python3-platformdirs all 4.4.0-1 [16.7 kB] Get: 290 http://deb.debian.org/debian forky/main amd64 python3-fs all 2.4.16-8 [95.2 kB] Get: 291 http://deb.debian.org/debian forky/main amd64 python3-lxml amd64 6.0.2-1 [1447 kB] Get: 292 http://deb.debian.org/debian forky/main amd64 python3-lz4 amd64 4.4.4+dfsg-3 [25.6 kB] Get: 293 http://deb.debian.org/debian forky/main amd64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 294 http://deb.debian.org/debian forky/main amd64 python3-scipy amd64 1.15.3-1.1 [17.0 MB] Get: 295 http://deb.debian.org/debian forky/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 296 http://deb.debian.org/debian forky/main amd64 python3-sympy all 1.14.0-2 [4228 kB] Get: 297 http://deb.debian.org/debian forky/main amd64 python3-attr all 25.4.0-1 [73.1 kB] Get: 298 http://deb.debian.org/debian forky/main amd64 python3-ufolib2 all 0.17.1+dfsg1-1 [33.0 kB] Get: 299 http://deb.debian.org/debian forky/main amd64 python3-unicodedata2 amd64 16.0.0+ds-1 [324 kB] Get: 300 http://deb.debian.org/debian forky/main amd64 python3-zopfli amd64 0.2.3.post1-1+b1 [10.5 kB] Get: 301 http://deb.debian.org/debian forky/main amd64 unicode-data all 16.0.0-1 [9197 kB] Get: 302 http://deb.debian.org/debian forky/main amd64 python3-fonttools amd64 4.57.0-2 [1457 kB] Get: 303 http://deb.debian.org/debian forky/main amd64 python3-kiwisolver amd64 1.4.7-3+b1 [62.0 kB] Get: 304 http://deb.debian.org/debian forky/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 305 http://deb.debian.org/debian forky/main amd64 python3-matplotlib amd64 3.10.1+dfsg1-6 [23.8 MB] Get: 306 http://deb.debian.org/debian forky/main amd64 python3-pyqt5.sip amd64 12.17.1-1 [61.7 kB] Get: 307 http://deb.debian.org/debian forky/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-3 [2537 kB] Get: 308 http://deb.debian.org/debian forky/main amd64 python3-ost amd64 2.11.1-1 [4043 kB] Get: 309 http://deb.debian.org/debian forky/main amd64 openstructure amd64 2.11.1-1 [93.1 MB] Fetched 356 MB in 6s (62.0 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 ... 19898 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.9-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.9-1_amd64.deb ... Unpacking python3.13-minimal (3.13.9-1) ... Setting up libpython3.13-minimal:amd64 (3.13.9-1) ... Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... 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 ... 20232 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_14.0.0_all.deb ... Unpacking media-types (14.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... 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_3.13.9-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.9-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.9-1_amd64.deb ... Unpacking python3.13 (3.13.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21247 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. 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Setting up libglu1-mesa:amd64 (9.0.2-1.1+b3) ... Setting up libicu76:amd64 (76.1-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgcc-14-dev:amd64 (14.3.0-8) ... Setting up libost-geom-dev (2.11.1-1) ... Setting up libost-base-dev (2.11.1-1) ... Setting up python-matplotlib-data (3.10.1+dfsg1-6) ... Setting up libwebpmux3:amd64 (1.5.0-0.1) ... Setting up libopenmm8.1 (8.1.2+dfsg-12) ... Setting up libstdc++-14-dev:amd64 (14.3.0-8) ... Setting up libdrm-common (2.4.125-2) ... Setting up libyuv0:amd64 (0.0.1919.20250919-1) ... 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 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:amd64 (1:19.1.7-7) ... 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+b1) ... 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 libost-mol2.11 (2.11.1-1) ... Setting up libwebpdemux2:amd64 (1.5.0-0.1) ... Setting up libost-mol-dev (2.11.1-1) ... 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 libost-conop2.11 (2.11.1-1) ... 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 libost-conop-dev (2.11.1-1) ... Setting up libboost-test-dev:amd64 (1.83.0.2+b2) ... Setting up dh-autoreconf (21) ... Setting up libglib2.0-0t64:amd64 (2.86.0-5) ... 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 shared-mime-info (2.4-5+b3) ... Setting up libp11-kit0:amd64 (0.25.9-2) ... 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) ... 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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 (3.13.9-1) ... 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 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 (3.13.9-1) ... 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 python3-fs (2.4.16-8) ... Setting up libqt5core5t64:amd64 (5.15.17+dfsg-4) ... Setting up python3-decorator (5.2.1-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-pyparsing (3.1.3-1) ... 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Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ... Setting up libqt5dbus5t64:amd64 (5.15.17+dfsg-4) ... Setting up python3-scipy (1.15.3-1.1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up libcurl4t64:amd64 (8.16.0-4) ... Setting up libgbm1:amd64 (25.2.5-1) ... Setting up python3-lz4 (4.4.4+dfsg-3) ... Setting up python3.13-dev (3.13.9-1) ... 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 (25.2.5-1) ... Setting up libqt5network5t64:amd64 (5.15.17+dfsg-4) ... Setting up libqt5xml5t64:amd64 (5.15.17+dfsg-4) ... Setting up python3-tk:amd64 (3.13.5-1) ... Setting up debhelper (13.28) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libqt5test5t64:amd64 (5.15.17+dfsg-4) ... Setting up python3-pil:amd64 (11.3.0-1) ... Setting up libegl-mesa0:amd64 (25.2.5-1) ... Setting up python3-pil.imagetk:amd64 (11.3.0-1) ... 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Setting up libqt5help5:amd64 (5.15.17-3) ... Setting up libost-gfx2.11 (2.11.1-1) ... Setting up libost-mol-alg-dev (2.11.1-1) ... Setting up libost-io2.11 (2.11.1-1) ... Setting up libqt5printsupport5t64:amd64 (5.15.17+dfsg-4) ... Setting up libost-gui2.11 (2.11.1-1) ... Setting up libqt5designer5:amd64 (5.15.17-3) ... Setting up libost-io-dev (2.11.1-1) ... Setting up libost-mol-mm2.11 (2.11.1-1) ... Setting up python3-pyqt5 (5.15.11+dfsg-3) ... Setting up libost-mol-mm-dev (2.11.1-1) ... Setting up python3-fonttools (4.57.0-2) ... Setting up python3-ufolib2 (0.17.1+dfsg1-1) ... Setting up python3-matplotlib (3.10.1+dfsg1-6) ... Setting up python3-ost (2.11.1-1) ... Setting up openstructure (2.11.1-1) ... 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/promod3-3.6.0+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_3.6.0+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.6.0+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/promod3-3.6.0+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 -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Found Python: /usr/bin/python3 (found suitable version "3.13.9", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") -- 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 (1.3s) -- 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.6.0+ds -B/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/config/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.6.0+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 -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+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 -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/extras /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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 core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/__init__.py make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/loop/__init__.py 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/scoring/__init__.py 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/sidechain/__init__.py make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.6.0+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib -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/promod3-3.6.0+ds/cmake_support/substitute.cmake make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-model /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] Generating ../../stage/lib/python3.13/site-packages/promod3/__init__.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_closegaps.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.6.0+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.6.0 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.6.0+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.6.0+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/cmake_support/substitute.cmake cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target scoring_pymod [ 1%] Built target loop_pymod cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 [ 1%] Built target config_header [ 1%] Built target sidechain_pymod [ 1%] Built target scoring_data_dir [ 1%] Built target sidechain_data_dir [ 1%] Built target loop_data_dir cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/pm3argparse.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_molprobity.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target subst_pm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-help /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_pipeline.py [ 1%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains [ 1%] Built target bash-completion make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin/pm make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target core_pymod cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_ring_punches.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin/pm make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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 -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 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_denovo.py [ 1%] Built target actions 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" [ 1%] Built target init_pymod make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_fragger_handle.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh [ 1%] Built target promod3_scripts cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./message.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh [ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh [ 1%] Built target promod3_core_headers cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.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/cluster.cc.o [ 2%] 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 [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/geom_base.cc [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/cluster.cc [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/geom_stems.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/superpose.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/graph.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/tree.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/src/tetrahedral_polytope.cc cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh [ 5%] Built target promod3_modelling_headers cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_sidechain_headers [ 5%] Built target promod3_scoring_headers [ 5%] Linking CXX shared library ../../stage/lib/libpromod3_core.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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.3.6 -o ../../stage/lib/libpromod3_core.so.3.6.0 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: /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 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_core.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6 ../../stage/lib/libpromod3_core.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 5%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o [ 5%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.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 cd /build/reproducible-path/promod3-3.6.0+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 -D_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/pymod/wrap_core.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_core_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/pymod/export_geom.cc cd /build/reproducible-path/promod3-3.6.0+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 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-I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/pymod/export_graph_minimizer.cc [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o [ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o [ 8%] Building CXX object 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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/promod3-3.6.0+ds/loop/src/amino_acid_atoms.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF 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/build/reproducible-path/promod3-3.6.0+ds/loop/src/bb_trace_param.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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 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/build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/hydrogen_constructor.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/idx_handler.cc cd 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loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/structure_db.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/loop_object_loader.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/psipred_prediction.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/mm_system_creator.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/torsion_sampler.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/sidechain_atom_constructor.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/src/sidechain_atom_rule_lookup.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/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:22, from /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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 constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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 module ../../stage/lib/python3.13/site-packages/promod3/core/_core.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_core.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libpromod3_core.so.3.6.0 /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 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core [ 19%] Linking CXX shared library ../../stage/lib/libpromod3_loop.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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.3.6 -o ../../stage/lib/libpromod3_loop.so.3.6.0 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: /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/lib/libpromod3_core.so.3.6.0 /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 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6 ../../stage/lib/libpromod3_loop.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Leaving 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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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_all_atom_positions.cc [ 25%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_amino_acid_atoms.cc [ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o [ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/disulfid.cc [ 28%] 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CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.6.0+ds/scoring/src/backbone_overall_scorer.cc [ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/bb_dep_rotamer_lib.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/frame.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/particle_scoring.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_all_atom_env.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_backbone.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/cbeta_env_listener.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_frag_db.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/scwrl4_particle_scoring.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_forcefield_lookup.cc cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK 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-DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/scwrl3_particle_scoring.cc cd /build/reproducible-path/promod3-3.6.0+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 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-DBOOST_PYTHON_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_loop_object_loader.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_mm_system_creator.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_psipred_prediction.cc [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o [ 35%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o [ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o [ 30%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o [ 43%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o [ 30%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/clash_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/wrap_loop.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/vina_particle_scoring.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_id.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_cruncher.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_lib.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/reduced_env_listener.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_torsion_sampler.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_lib_reader.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/loop/pymod/export_structure_db.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_density.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/scoring_object_loader.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_group.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_lib_entry.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/cb_packing_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/cbeta_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/reduced_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/clash_env_listener.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/density_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/hbond_env_listener.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/hbond_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/ss_agreement_score.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/sidechain_object_loader.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/sidechain_connector.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/ss_agreement_env_listener.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_constructor.cc [ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/rotamer_lookup.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/torsion_score.cc [ 47%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/pairwise_score.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/all_atom_overall_scorer.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/scwrl3_rotamer_constructor.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/vina_rotamer_constructor.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/all_atom_interaction_env_listener.cc [ 50%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/src/subrotamer_optimizer.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/all_atom_interaction_score.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/all_atom_packing_score.cc [ 53%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/src/all_atom_clash_score.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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/loop/pymod/export_all_atom_env.cc: In function 'promod3::loop::AllAtomEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.6.0+ds/loop/pymod/export_all_atom_env.cc:52:56: note: '' declared here 52 | String s = boost::python::extract(seqres[i]); | ^ 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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/loop/pymod/export_mm_system_creator.cc:18: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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])); | ^~~~~~~~~~~~~~~~ [ 53%] Linking CXX shared library ../../stage/lib/libpromod3_scoring.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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.3.6 -o ../../stage/lib/libpromod3_scoring.so.3.6.0 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: /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/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_scoring.so.3.6.0 ../../stage/lib/libpromod3_scoring.so.3.6 ../../stage/lib/libpromod3_scoring.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.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_backbone_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_scwrl3_energy_functions.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_backbone_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_all_atom_score.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_object_loader.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_pairwise_functions.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_constraint_constructor.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/export_density_scorer.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/pymod/wrap_scoring.cc [ 60%] Linking CXX shared library ../../stage/lib/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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.3.6 -o ../../stage/lib/libpromod3_sidechain.so.3.6.0 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: /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/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_sidechain.so.3.6.0 ../../stage/lib/libpromod3_sidechain.so.3.6 ../../stage/lib/libpromod3_sidechain.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/gap_extender.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong 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-D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/pymod/export_frame.cc [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o [ 74%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o [ 76%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o [ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/monte_carlo.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/pymod/export_rotamer.cc [ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall 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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/promod3-3.6.0+ds/modelling/src/ccd.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF 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-o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/reproducible-path/promod3-3.6.0+ds/modelling/src/extension_scheme.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/pymod/export_rotamer_cruncher.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/kic.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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 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CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod/export_rotamer_constructor.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF 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CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.6.0+ds/modelling/src/score_container.cc cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/src/afdb.cc [ 81%] Linking CXX shared module ../../stage/lib/python3.13/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_loop.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libpromod3_loop.so.3.6.0 /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/lib/libpromod3_core.so.3.6.0 /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 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 81%] Built target _loop 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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/scoring/pymod/export_all_atom_score.cc:18: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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 'void promod3::core::ConvertDictToMap(const boost::python::dict&, std::map&) [with K = std::__cxx11::basic_string; V = float]' at /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/scoring/pymod/export_backbone_score.cc:18: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)' at /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/scoring/pymod/export_backbone_score.cc: In function 'promod3::scoring::BackboneScoreEnvPtr {anonymous}::WrapInitStrList(const boost::python::list&)': /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod/export_backbone_score.cc:59:58: note: '' declared here 59 | String s = boost::python::extract(seqres[i]); | ^ [ 81%] Linking CXX shared module ../../stage/lib/python3.13/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_scoring.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libpromod3_scoring.so.3.6.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/reproducible-path/promod3-3.6.0+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/lib/python3.13/site-packages/promod3/sidechain/_sidechain.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_sidechain.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib/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 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/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_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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.3.6 -o ../../stage/lib/libpromod3_modelling.so.3.6.0 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: /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/lib/libpromod3_scoring.so.3.6.0 ../../stage/lib/libpromod3_sidechain.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib/libpromod3_modelling.so.3.6.0 ../../stage/lib/libpromod3_modelling.so.3.6 ../../stage/lib/libpromod3_modelling.so make[3]: Leaving directory 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CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/export_loop_closure.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_model.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_score_container.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_scoring_weights.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_rigid_blocks.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_sidechain_reconstructor.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/export_motif_finder.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/pymod/wrap_modelling.cc cd /build/reproducible-path/promod3-3.6.0+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 -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_scoring_weights.cc:19: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_score_container.cc:19: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc:21: /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::SoftInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::FragmentInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc: In function 'boost::python::api::object {anonymous}::PhiPsiInitWrapper(boost::python::tuple, boost::python::dict)': /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/export_monte_carlo.cc:47:39: note: '' declared here 47 | String seq = extract(args[0]); | ^ [ 90%] Linking CXX shared module ../../stage/lib/python3.13/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,--dependency-file=CMakeFiles/_modelling.dir/link.d -Wl,-z,relro -shared -o ../../stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib: ../../stage/lib/libpromod3_modelling.so.3.6.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../stage/lib/libpromod3_scoring.so.3.6.0 ../../stage/lib/libpromod3_sidechain.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data 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cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" make 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'/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake "--color=" 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds 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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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" 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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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 -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+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]: Entering directory '/build/reproducible-path/promod3-3.6.0+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]: Entering directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+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]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+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 -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 -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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat [ 91%] Generating ../../stage/share/promod3/sidechain_data/lib.dat [ 91%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat [100%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat [100%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat [ 95%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat [100%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat [100%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat [100%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.6.0+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.6.0+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.6.0+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer 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. Compound library not available. Some functionality may not work as expected. /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_hbond_scorer.dat [100%] Built target generate_scoring_data_cb_packing_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_aa_scorer.dat [100%] Built target generate_scoring_data_cbeta_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_coil.dat [100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_ff_lookup_charmm.dat [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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" [100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data [100%] Built target generate_loop_data_torsion_sampler_extended.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_ss_agreement_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_helical.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat [100%] Built target generate_scoring_data_aa_packing_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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.6.0+ds -B/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.6.0+ds -B/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-model /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-help /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/tests/data/gly.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/tests/data/seq.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/actions/tests/data/seq_ins.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 1%] running checks test_actions.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests//test_helper.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/broken_on_purpose.chemlib /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/1crn.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2jlp-1.json /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/1crn.hhm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/alignment.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake_1.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake_2trg.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake_3.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake.fas.gz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake_nel.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/tests/data/fasta/1ake_sw.fas /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./message.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/config/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/core/tests/tests.cc [ 6%] Linking CXX executable ../../tests/core/test_suite_core cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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 make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/__init__.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/core/pm3argparse.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 9%] running checks for module core cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 10%] running checks test_setcompoundschemlib.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/core/tests/test_setcompoundschemlib.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.322s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_pm3argparse.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/core/tests/test_pm3argparse.py" Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- Ran 66 tests in 2.269s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/__init__.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/modelling/_afdb_modelling.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/loop/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/scoring/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages//promod3/sidechain/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/1A88A.hhm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/1A88A.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/1A88A_with_gap.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/1akyA.horiz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/all_aa.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/all_aa_prot_ref.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/loop/tests/data/CHARMM27.dat /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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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-I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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 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'/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 84%] running checks for module loop cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/tests/data/1CRNA.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/scoring/tests/data/clash_test.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/tests/test_all_atom_scorer.cc /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/scoring/tests/tests.cc [ 89%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib/libpromod3_scoring.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 90%] running checks for module scoring cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/sidechain cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/sidechain/tests/data/all_sc.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/tests/test_rotamers.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o cd /build/reproducible-path/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/sidechain/tests/tests.cc [ 93%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib/libpromod3_sidechain.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 93%] running checks for module sidechain cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1cjx-1.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1cjx-1.pdb.gz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_build.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_final.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_rec.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_sc.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1crn_sc_test.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1CRNA.hhm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1eye.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1eye_rec.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1eye_sc_test.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/1mcg.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2dbs.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2jlp-1.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2jlp-1.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2xim-1.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/2xim-1.pdb.gz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/3b08-3.pdb.gz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/3b08-3.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/4ksl-1.pdb.gz /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/4ksl-1.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/5d52-1.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/5d52-1_cut.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/CA-3cm91E.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/CA-3cm91E.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/cbeta.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/cbeta.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/del.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/ff_NAD.dat /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/gly.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/gly_on_top.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/gly_almost_on_top.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/gly_shifted_nter.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/hetero-punched.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/ins.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/neighbor-punched.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/port_frag_db.dat /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/port_str_db.dat /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/sep.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/sep.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/seq.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/smtl2bl4.1.pdb /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/ter.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/data/double_gap_aln.fasta /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+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/promod3-3.6.0+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_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/modelling/tests/tests.cc [ 95%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -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/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib/libpromod3_modelling.so.3.6.0 ../../stage/lib/libpromod3_scoring.so.3.6.0 ../../stage/lib/libpromod3_sidechain.so.3.6.0 ../../stage/lib/libpromod3_loop.so.3.6.0 ../../stage/lib/libpromod3_core.so.3.6.0 /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_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks for module modelling cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_close_gaps.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/test_close_gaps.py" Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- Ran 33 tests in 23.002s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_gap_extension.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/test_gap_extension.py" Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- Ran 6 tests in 0.021s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_modelling.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+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 0.106s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_pipeline.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+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 40.416s 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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_ring_punches.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/test_ring_punches.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.125s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_sidechain_reconstruction.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/test_sidechain_reconstruction.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 2.099s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/modelling/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_alignment_fiddling.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/modelling/tests/test_alignment_fiddling.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.012s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.6.0+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib -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/promod3-3.6.0+ds/cmake_support/substitute.cmake make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/bin/pm make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-model.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/actions/tests/test_action_build-model.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 5.135s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-rawmodel.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/actions/tests/test_action_build-rawmodel.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 1.341s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/actions/tests /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] running checks test_action_help.py cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/stage/lib/python3.13/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.6.0+ds/actions/tests/test_action_help.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.031s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/promod3-3.6.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.6.0+ds -B/build/reproducible-path/promod3-3.6.0+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/promod3-3.6.0+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_core.so.3.6.0 -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_core.so.3.6 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_core.so.3.6.0" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_core.so -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/check_io.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/cluster.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/dynamic_spatial_organizer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/export_helper.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/geom_base.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/geom_stems.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/message.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/portable_binary_data_sink.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/portable_binary_data_source.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/portable_binary_serializer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/runtime_profiling.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/superpose.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/enumerator.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/graph.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/tree.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/tetrahedral_polytope.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/graph_minimizer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/core/eigen_types.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/core/_core.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/core/_core.so" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/core/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/core/helper.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/core/pm3argparse.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_loop.so.3.6.0 -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_loop.so.3.6 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_loop.so.3.6.0" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_loop.so -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/all_atom_env.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/all_atom_positions.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/amino_acid_atoms.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/backbone.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/bb_trace_param.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/data_bag.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/dense_hash_table.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/dense_map.hh -- Up-to-date: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/dense_map.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/density_creator.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/forcefield_lookup.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/frag_db.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/fragger.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/hydrogen_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/hydrogen_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/idx_handler.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/loop_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/mm_system_creator.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/psipred_prediction.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/stem_geom.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/structure_db.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/torsion_sampler.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/ushort_vec.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/sidechain_atom_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/sidechain_atom_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/loop/structure_db_custom_types.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/loop/_loop.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/loop/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_scoring.so.3.6.0 -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_scoring.so.3.6 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_scoring.so.3.6.0" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_scoring.so -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/backbone_score_base.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/backbone_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/scoring_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/cbeta_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/cb_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/cbeta_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/reduced_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/reduced_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/clash_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/clash_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/density_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/hbond_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/hbond_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/ss_agreement_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/ss_agreement_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/torsion_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/pairwise_scoring_function.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/pairwise_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/constraint_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_score_base.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_interaction_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_interaction_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/all_atom_clash_score.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/scoring/scwrl3_energy_functions.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/scoring/_scoring.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/scoring/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_sidechain.so.3.6.0 -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_sidechain.so.3.6 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_sidechain.so.3.6.0" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_sidechain.so -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/bb_dep_rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/disulfid.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/frame.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_graph.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/particle.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/particle_scoring_base.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/scwrl4_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/scwrl3_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/vina_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_cruncher.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_density.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_group.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_id.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_lib_entry.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_lib_reader.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/sidechain_connector.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/sidechain_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/rotamer_lookup.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/scwrl4_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/scwrl3_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/vina_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/sidechain/subrotamer_optimizer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/sidechain/_sidechain.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/sidechain/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_modelling.so.3.6.0 -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_modelling.so.3.6 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_modelling.so.3.6.0" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/libpromod3_modelling.so -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/extension_scheme.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/gap.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/gap_extender.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/model.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/all_atom_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/backbone_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/ccd.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/kic.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/loop_candidate.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/monte_carlo.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/monte_carlo_closer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/monte_carlo_cooler.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/monte_carlo_sampler.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/monte_carlo_scorer.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/rigid_blocks.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/score_container.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/scoring_weights.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/sidechain_reconstructor.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/sidechain_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/motif_finder.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/robin_hood.h -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/include/promod3/modelling/afdb.hh -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_modelling.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/__init__.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_denovo.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_planar_rings.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/lib/python3.13/site-packages/promod3/modelling/_afdb_modelling.py -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/bin/pm -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/reproducible-path/promod3-3.6.0+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+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-${PKG}-dev usr/lib/libpromod3_${PKG}.so usr/lib/x86_64-linux-gnu; \ dh_install -p libpromod3-${PKG}3.6 usr/lib/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/promod3-3.6.0+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib make[1]: Leaving directory '/build/reproducible-path/promod3-3.6.0+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:421: renaming _sidechain.so to _sidechain.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 _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 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_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.6' in '../libpromod3-core3.6_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.6-dbgsym' in '../libpromod3-core3.6-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.6' in '../libpromod3-loop3.6_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.6-dbgsym' in '../libpromod3-loop3.6-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.6' in '../libpromod3-modelling3.6_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.6-dbgsym' in '../libpromod3-modelling3.6-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.6' in '../libpromod3-scoring3.6_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.6-dbgsym' in '../libpromod3-scoring3.6-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.6' in '../libpromod3-sidechain3.6_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.6-dbgsym' in '../libpromod3-sidechain3.6-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.6.0+ds-1_all.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.6.0+ds-1_all.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.6.0+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.6.0+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.6.0+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.6.0+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: not including original 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/1521066 and its subdirectories I: Current time: Mon Nov 23 14:45:59 -12 2026 I: pbuilder-time-stamp: 1795488359 Tue Oct 21 20:23:03 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Tue Oct 21 20:23:03 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Tue Oct 21 20:33:02 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Tue Oct 21 20:33:02 UTC 2025 I: promod3_3.6.0+ds-1_amd64.changes: Format: 1.8 Date: Thu, 16 Oct 2025 02:50:26 -0400 Source: promod3 Binary: libpromod3-core-dev libpromod3-core3.6 libpromod3-core3.6-dbgsym libpromod3-loop-dev libpromod3-loop3.6 libpromod3-loop3.6-dbgsym libpromod3-modelling-dev libpromod3-modelling3.6 libpromod3-modelling3.6-dbgsym libpromod3-scoring-dev libpromod3-scoring3.6 libpromod3-scoring3.6-dbgsym libpromod3-sidechain-dev libpromod3-sidechain3.6 libpromod3-sidechain3.6-dbgsym promod3 promod3-data python3-promod3 python3-promod3-dbgsym Architecture: amd64 all Version: 3.6.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libpromod3-core-dev - protein homology modelling engine libpromod3-core3.6 - protein homology modelling engine libpromod3-loop-dev - protein homology modelling engine libpromod3-loop3.6 - protein homology modelling engine libpromod3-modelling-dev - protein homology modelling engine libpromod3-modelling3.6 - protein homology modelling engine libpromod3-scoring-dev - protein homology modelling engine libpromod3-scoring3.6 - protein homology modelling engine libpromod3-sidechain-dev - protein homology modelling engine libpromod3-sidechain3.6 - 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 (3.6.0+ds-1) unstable; urgency=medium . * Upload to unstable. Checksums-Sha1: 096aa8eca0cb58010ba338487c14c060483cabea 24652 libpromod3-core-dev_3.6.0+ds-1_amd64.deb 14296f21db5cbc966c0983e1d96a2968060e1632 2628384 libpromod3-core3.6-dbgsym_3.6.0+ds-1_amd64.deb b524acd0163b027fcdd82476bc5d8afc051d722f 96448 libpromod3-core3.6_3.6.0+ds-1_amd64.deb 31d29991bf90f7a76e4c006a518b02b1cbd6214a 35644 libpromod3-loop-dev_3.6.0+ds-1_amd64.deb 8078ab2abb941fd3d26d06aa511b6de0cf6680bd 5300392 libpromod3-loop3.6-dbgsym_3.6.0+ds-1_amd64.deb 01368580fe15ab52a3ee34b06148efee6aad3c75 285168 libpromod3-loop3.6_3.6.0+ds-1_amd64.deb 6d872ca64c0dacd43f2df5ba29acbee8d54b0ec5 37224 libpromod3-modelling-dev_3.6.0+ds-1_amd64.deb 5b9b0fe84c95e5b46c5597d13e0bdc11756f3e18 12192796 libpromod3-modelling3.6-dbgsym_3.6.0+ds-1_amd64.deb 414817e1b34cef2d1e41ba29364c2cecf58202ef 310100 libpromod3-modelling3.6_3.6.0+ds-1_amd64.deb 522fe2116e765f3865a51264eff8003ecd25de09 18256 libpromod3-scoring-dev_3.6.0+ds-1_amd64.deb 070ea87cdea6d7b942263a8c4bab1253010c7af2 4608532 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ea1fb14afc8f887f59cc5269ced6761e0c184a4b575d60c4f5ee5fe6c099c9a4 19249028 python3-promod3-dbgsym_3.6.0+ds-1_amd64.deb 278a07d6e9f14faa3e360ac24b1b0b39225099bd95c641c97561a9d13369c872 1064132 python3-promod3_3.6.0+ds-1_amd64.deb Files: 9d0d02a9fa0914cc3d05bf478855575b 24652 libdevel optional libpromod3-core-dev_3.6.0+ds-1_amd64.deb 8fea81956175a8411eb60298a2685f61 2628384 debug optional libpromod3-core3.6-dbgsym_3.6.0+ds-1_amd64.deb e2211a14a33d85a30a70b501d9a378d0 96448 libs optional libpromod3-core3.6_3.6.0+ds-1_amd64.deb 434b26ef7cd713f6736bd13ec088e665 35644 libdevel optional libpromod3-loop-dev_3.6.0+ds-1_amd64.deb 59639d81dbbac62dac793d0be1a170af 5300392 debug optional libpromod3-loop3.6-dbgsym_3.6.0+ds-1_amd64.deb 2840a53d3a4fef0ae3b0c2efe708edd6 285168 libs optional libpromod3-loop3.6_3.6.0+ds-1_amd64.deb a93af0d1d6985542215fbd3e9c34272c 37224 libdevel optional libpromod3-modelling-dev_3.6.0+ds-1_amd64.deb a75b1a717fb3355450b540f3324a4b5e 12192796 debug optional libpromod3-modelling3.6-dbgsym_3.6.0+ds-1_amd64.deb 957567bbc11f18a4e5277efd39791457 310100 libs optional libpromod3-modelling3.6_3.6.0+ds-1_amd64.deb 4fde17ca556e32b2d392b3eb93029bb4 18256 libdevel optional libpromod3-scoring-dev_3.6.0+ds-1_amd64.deb 2ba8becedec1910adca32d5512489782 4608532 debug optional libpromod3-scoring3.6-dbgsym_3.6.0+ds-1_amd64.deb f4d12ba9e7f3a336f5f65ad623604eba 183076 libs optional libpromod3-scoring3.6_3.6.0+ds-1_amd64.deb 40abfca8d5ad850558103b19ffcf470a 19592 libdevel optional libpromod3-sidechain-dev_3.6.0+ds-1_amd64.deb 4cdb8272ab7f25cd36e026f75d709e93 4473256 debug optional libpromod3-sidechain3.6-dbgsym_3.6.0+ds-1_amd64.deb 36e2b0948d318b81d1052c6ca0252d67 237964 libs optional libpromod3-sidechain3.6_3.6.0+ds-1_amd64.deb 8483123de15ef1447dadc6996803063c 371364144 science optional promod3-data_3.6.0+ds-1_all.deb ade863b59cc4cdb65c5850a21287593f 11196 science optional promod3_3.6.0+ds-1_all.deb ceb2428f34253a0ebc663dfd5b194644 19064 science optional promod3_3.6.0+ds-1_amd64.buildinfo ca9dd6762f482ed8e39123392f876c3b 19249028 debug optional python3-promod3-dbgsym_3.6.0+ds-1_amd64.deb 995e6316de2816c508e43aaa7e1a5d9d 1064132 python optional python3-promod3_3.6.0+ds-1_amd64.deb Tue Oct 21 20:33:03 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_20-70952.service; invocation ID: 8417aac59170423fb5d0551248029d7c # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/promod3_3.6.0+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/promod3_3.6.0+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/promod3_3.6.0+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/b1/promod3_3.6.0+ds-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2ngCPHIK/b2/promod3_3.6.0+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: 209ms CPU time consumed: 172ms Memory peak: 17.9M (swap: 0B) Tue Oct 21 20:33:06 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 21 20:33:06 UTC 2025 I: promod3 from forky built successfully and reproducibly on amd64. Tue Oct 21 20:33:06 UTC 2025 I: Removing signed promod3_3.6.0+ds-1_amd64.buildinfo.asc files: removed './b1/promod3_3.6.0+ds-1_amd64.buildinfo.asc' removed './b2/promod3_3.6.0+ds-1_amd64.buildinfo.asc'