Fri May 31 02:02:17 UTC 2024 I: starting to build promod3/unstable/amd64 on jenkins on '2024-05-31 02:02' Fri May 31 02:02:17 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/14526/console.log Fri May 31 02:02:17 UTC 2024 I: Downloading source for unstable/promod3=3.4.0+ds-1 --2024-05-31 02:02:18-- http://deb.debian.org/debian/pool/main/p/promod3/promod3_3.4.0%2bds-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3223 (3.1K) [text/prs.lines.tag] Saving to: ‘promod3_3.4.0+ds-1.dsc’ 0K ... 100% 335M=0s 2024-05-31 02:02:18 (335 MB/s) - ‘promod3_3.4.0+ds-1.dsc’ saved [3223/3223] Fri May 31 02:02:18 UTC 2024 I: promod3_3.4.0+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: promod3 Binary: libpromod3-core-dev, libpromod3-core3.4, libpromod3-loop-dev, libpromod3-loop3.4, libpromod3-modelling-dev, libpromod3-modelling3.4, libpromod3-scoring-dev, libpromod3-scoring3.4, libpromod3-sidechain-dev, libpromod3-sidechain3.4, promod3, promod3-data, python3-promod3 Architecture: any all Version: 3.4.0+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, openstructure (>= 2.5.0), python3-dev, python3-ost Package-List: libpromod3-core-dev deb libdevel optional arch=any libpromod3-core3.4 deb libs optional arch=any libpromod3-loop-dev deb libdevel optional arch=any libpromod3-loop3.4 deb libs optional arch=any libpromod3-modelling-dev deb libdevel optional arch=any libpromod3-modelling3.4 deb libs optional arch=any libpromod3-scoring-dev deb libdevel optional arch=any libpromod3-scoring3.4 deb libs optional arch=any libpromod3-sidechain-dev deb libdevel optional arch=any libpromod3-sidechain3.4 deb libs optional arch=any promod3 deb science optional arch=all promod3-data deb science optional arch=all python3-promod3 deb python optional arch=any Checksums-Sha1: 144585f28c78c9b83e1a8a672d5f70e036518690 398763688 promod3_3.4.0+ds.orig.tar.xz 9928ae8ec2ea3720c6e5255c1ec69140d20fc413 5796 promod3_3.4.0+ds-1.debian.tar.xz Checksums-Sha256: 1ae5827dbae0de2b683927ad8b9ca8f527742db32acf868dbab1b9eecaa1058f 398763688 promod3_3.4.0+ds.orig.tar.xz 505417ee5fa790b4315c346b2b975f9edff9abaf65930de2fbc57c0c0a38c15a 5796 promod3_3.4.0+ds-1.debian.tar.xz Files: a379bcb03a563d1c034f8ec399e1fdcf 398763688 promod3_3.4.0+ds.orig.tar.xz 03ae3ec250d874c9fc96cd82509c8d9b 5796 promod3_3.4.0+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmWyEykSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHnx4P/ArkS+5j6TbTeGSTYdxSSF99o4XqOQu6 hweEOTvmyjPgUrx7PO6JJAZ4fzTIAAeciJHET4iJKHq+kgorB2Gbkw7GiRWNTRdr 68q6oiO7hMpDasWq9tWtWDro3XTqBf/Iai3pjk5kvjPDdY/QtbzWKy8HBgTvv+wS 0l1P8kosfx067GnVz8kpFHnHZY337bsUdO8PwNcpS7nk9keyAMLEKmRjalOGb3QT 0xxZ76ZsgJw9Jb7gTmVm5SNIj9dWezLCKjM8qpj70ZoSAJ2fckYvOgesit37UUSY iLl8OxM9qoU+QvTyPLIpaRgvcjN8bBqRuzfOcz8Ew50CvFzhIx45rhQ6UzeJ/1oY YehTu3LlMRcSQk8r3UHtXzn0vQa9Gqcnma5RBFHaCp2O/1thju6oetBzGERqIc4h Yx1K8UAwOQSJc+AbSoEt9UbrTHwUeDACmG9fpWLRaYYuU5HTb43mxzMb5T/iAxtK 1muz3C3AOTt21DWKVCv9+8fOblxqzgpj6AiXGTgP4TvoSF04vHzt9LGDyKaj5LGY zqEYcCohUbBaKjGyzukTyUwe1MVY+AUgDYDQvXNVxw5EtaqWcMPwl+px/FglTI5N W5sab0bluNbAbf5Yxrq27FIJVwXI/0FVQD7lt123f3v90vSEmUuDR+WG0PyZg45o kwh4Rzco+ZHv =3UjO -----END PGP SIGNATURE----- Fri May 31 02:02:18 UTC 2024 I: Checking whether the package is not for us Fri May 31 02:02:18 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Fri May 31 02:02:18 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Fri May 31 02:15:08 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 2 20:25:24 -12 2025 I: pbuilder-time-stamp: 1751531124 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [promod3_3.4.0+ds-1.dsc] I: copying [./promod3_3.4.0+ds.orig.tar.xz] I: copying [./promod3_3.4.0+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 25 07:52:09 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./promod3_3.4.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.4.0+ds dpkg-source: info: unpacking promod3_3.4.0+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.4.0+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/3810101/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='71341c6cfb794daa8e410ab63ea76eff' 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='3810101' 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.FTYUhzZi/pbuilderrc_3o0p --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/b1 --logfile b1/build.log promod3_3.4.0+ds-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 30 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3810101/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, 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 ... 19716 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 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} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{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} libbsd0{a} libcom-err2{a} libcups2t64{a} libcurl4t64{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1t64{a} libevdev2{a} libexpat1{a} libexpat1-dev{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgfortran5{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0t64{a} libglu1-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgudev-1.0-0{a} libharfbuzz0b{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17t64{a} libmagic-mgc{a} libmagic1t64{a} libmd4c0{a} libmtdev1t64{a} libnghttp2-14{a} libopengl0{a} libopenjp2-7{a} libopenmm8.1{a} libost-base-dev{a} libost-base2.5{a} libost-bindings2.5{a} libost-conop-dev{a} libost-conop2.5{a} libost-db2.5{a} libost-geom-dev{a} libost-geom2.5{a} libost-gfx2.5{a} libost-gui2.5{a} libost-img-alg2.5{a} libost-img-dev{a} libost-img2.5{a} libost-info-dev{a} libost-info2.5{a} libost-io-dev{a} libost-io2.5{a} libost-mol-alg-dev{a} libost-mol-alg2.5{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.5{a} libost-mol2.5{a} libost-seq-alg-dev{a} libost-seq-alg2.5{a} libost-seq-dev{a} libost-seq2.5{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} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{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} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{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-appdirs{a} python3-attr{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-ost{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-unicodedata2{a} python3.11{a} python3.11-dev{a} python3.11-minimal{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 javascript-common krb5-locales libarchive-cpio-perl libcifpp-data libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib python3-olefile qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 297 newly installed, 0 to remove and 0 not upgraded. Need to get 314 MB of archives. After unpacking 1202 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-4 [95.7 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b1 [17.0 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 53 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 60 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1+b1 [10.7 MB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 81 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-3.1 [77.7 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-3.1 [131 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1 [463 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-4+b1 [208 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-3 [10.6 MB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-3 [233 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-3 [235 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-3 [280 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-3 [230 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-3 [231 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-3 [295 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 108 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-3 [324 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-4+b1 [10.4 MB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-3 [342 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-3 [260 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 113 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-3 [345 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-3 [373 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 116 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83.0 amd64 1.83.0-3 [351 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 122 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-8 [150 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libboost-python1.83-dev amd64 1.83.0-3 [379 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-3 [466 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-3 [536 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libboost-test-dev amd64 1.83.0.2+b2 [3628 B] Get: 132 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-3 [269 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 137 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2 [116 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.0.8-1 [40.9 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.8-1 [36.5 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1+b1 [232 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2 [106 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2 [107 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2 [105 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2 [108 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2 [109 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b1 [8852 B] Get: 156 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 24.0.8-1 [119 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.1+dfsg-1+b1 [32.6 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-1+b2 [806 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.1.0-1 [836 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b1 [56.3 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2 [122 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2 [105 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b1 [20.3 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.283.0-1 [125 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.8-1 [8284 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.8-1 [151 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b1 [35.0 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b1 [89.8 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-2 [1485 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b1 [31.1 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b1 [180 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-5 [14.4 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.10.0-2 [62.5 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.10.0-2 [22.4 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.25.0-1+b2 [24.8 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.6-1.2 [22.2 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.25.0-1+b2 [128 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.1+dfsg-1 [1034 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 libost-base2.5 amd64 2.5.0-2+b1 [31.4 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libost-base-dev amd64 2.5.0-2+b1 [25.8 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libost-geom2.5 amd64 2.5.0-2+b1 [62.4 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libost-mol2.5 amd64 2.5.0-2+b1 [380 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5 [758 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.13+dfsg-2 [1837 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.13+dfsg-2 [124 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 libost-info2.5 amd64 2.5.0-2+b1 [161 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 libost-seq2.5 amd64 2.5.0-2+b1 [87.8 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 libost-bindings2.5 amd64 2.5.0-2+b1 [187 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 libost-conop2.5 amd64 2.5.0-2+b1 [182 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 libost-conop-dev amd64 2.5.0-2+b1 [19.9 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 libost-db2.5 amd64 2.5.0-2+b1 [43.9 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 libost-geom-dev amd64 2.5.0-2+b1 [26.8 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 libost-img2.5 amd64 2.5.0-2+b1 [141 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 libost-img-alg2.5 amd64 2.5.0-2+b1 [167 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 libost-gfx2.5 amd64 2.5.0-2+b1 [420 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg2.5 amd64 2.5.0-2+b1 [335 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libost-io2.5 amd64 2.5.0-2+b1 [723 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg2.5 amd64 2.5.0-2+b1 [247 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b1 [34.3 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.13+dfsg-2 [214 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.13+dfsg-2 [678 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2 [115 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2 [105 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2 [105 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2 [130 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2 [129 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.41-2 [795 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.6.0-1+b1 [109 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b1 [16.2 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.13+dfsg-2 [3450 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.13+dfsg-2 [2380 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 libost-gui2.5 amd64 2.5.0-2+b1 [500 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 libost-img-dev amd64 2.5.0-2+b1 [41.4 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 libost-info-dev amd64 2.5.0-2+b1 [18.6 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 libost-io-dev amd64 2.5.0-2+b1 [47.2 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 libost-mol-alg-dev amd64 2.5.0-2+b1 [29.0 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 libost-mol-dev amd64 2.5.0-2+b1 [55.7 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm2.5 amd64 2.5.0-2+b1 [279 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libost-mol-mm-dev amd64 2.5.0-2+b1 [26.6 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libost-seq-alg-dev amd64 2.5.0-2+b1 [177 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libost-seq-dev amd64 2.5.0-2+b1 [22.7 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.13-3 [2751 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.13+dfsg-2 [123 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.13-3 [150 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.13+dfsg-2 [204 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.13+dfsg-2 [149 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1+b1 [232 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.6.3-2 [2744 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.3-3.1 [113 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [5465 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.11.4-10 [19.5 MB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.12-8 [3869 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.6.3-2 [8167 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5.sip amd64 12.13.0-1+b1 [79.5 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-pyqt5 amd64 5.15.10+dfsg-1+b2 [2501 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-ost amd64 2.5.0-2+b1 [3868 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 openstructure amd64 2.5.0-2+b1 [93.1 MB] Fetched 314 MB in 10s (32.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19716 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20032 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21024 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../005-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.40.1-4_amd64.deb ... Unpacking bsdextrautils (2.40.1-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up libost-base-dev (2.5.0-2+b1) ... Setting up libsm6:amd64 (2:1.2.3-1+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2) ... Setting up libavahi-client3:amd64 (0.8-13+b2) ... Setting up libboost-filesystem-dev:amd64 (1.83.0.2+b2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2) ... Setting up libinput10:amd64 (1.25.0-1+b2) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1+b1) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up libgbm1:amd64 (24.0.8-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.8-1) ... Setting up libost-mol-dev (2.5.0-2+b1) ... Setting up libpython3.11t64:amd64 (3.11.9-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libost-conop-dev (2.5.0-2+b1) ... Setting up libqt5core5t64:amd64 (5.15.13+dfsg-2) ... Setting up libegl-mesa0:amd64 (24.0.8-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libegl1:amd64 (1.7.0-1+b1) ... Setting up libqt5sql5t64:amd64 (5.15.13+dfsg-2) ... Setting up cmake (3.29.3-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libqt5dbus5t64:amd64 (5.15.13+dfsg-2) ... Setting up libglx-mesa0:amd64 (24.0.8-1) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up libglx0:amd64 (1.7.0-1+b1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up libqt5network5t64:amd64 (5.15.13+dfsg-2) ... Setting up libqt5xml5t64:amd64 (5.15.13+dfsg-2) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up libqt5test5t64:amd64 (5.15.13+dfsg-2) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up libgl1:amd64 (1.7.0-1+b1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3-pyqt5.sip (12.13.0-1+b1) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-lib2to3 (3.12.3-3.1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-3.1) ... Setting up python3-sympy (1.12-8) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up libost-info2.5 (2.5.0-2+b1) ... Setting up python3-tk:amd64 (3.12.3-3.1) ... Setting up python3-fs (2.4.16-4) ... Setting up libqt5gui5t64:amd64 (5.15.13+dfsg-2) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-dev (3.11.8-1) ... 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Setting up libqt5printsupport5t64:amd64 (5.15.13+dfsg-2) ... Setting up libost-img-dev (2.5.0-2+b1) ... Setting up libqt5designer5:amd64 (5.15.13-3) ... Setting up libost-seq-alg-dev (2.5.0-2+b1) ... Setting up libost-mol-mm2.5 (2.5.0-2+b1) ... Setting up python3-pyqt5 (5.15.10+dfsg-1+b2) ... Setting up libost-mol-mm-dev (2.5.0-2+b1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-matplotlib (3.6.3-2) ... Setting up python3-ost (2.5.0-2+b1) ... Setting up openstructure (2.5.0-2+b1) ... Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/promod3-3.4.0+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_3.4.0+ds-1_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.4.0+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/promod3-3.4.0+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 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 13.2.0 -- The C compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done CMake Warning (dev) at CMakeLists.txt:58 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done CMake Warning (dev) at cmake_support/PROMOD3.cmake:980 (exec_program): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): cmake_support/PROMOD3.cmake:997 (get_compiler_version) CMakeLists.txt:87 (setup_compiler_flags) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python311 -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: unit_test_framework -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: filesystem system -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: iostreams -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: program_options -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.53") found components: regex -- Found Eigen3: /usr/include/eigen3 (Required is at least version "3.3.0") -- ProMod3 will be built with the following options: OpenStructure (-DOST_ROOT) : /usr Compound library (-DCOMPOUND_LIB): /var/cache/openstructure/compounds.chemlib Optimized (-DOPTIMIZE) : ON Python : /usr/bin/python3 Eigen3 : /usr/include/eigen3 -- Configuring done (2.1s) -- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.0+ds -B/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/promod3-3.4.0+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 -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && 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'/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/__init__.py make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.0+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.0+ds/cmake_support/substitute.cmake [ 1%] Generating ../../stage/lib64/python3.11/site-packages/promod3/__init__.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.0+ds/core/init/__init__.py.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/promod3/__init__.py -DOST_COMPOUNDS_CHEMLIB_PATH="\"/var/cache/openstructure/compounds.chemlib\"" -DOST_ROOT=/usr -DPROMOD3_VERSION_STRING=3.4.0 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/reproducible-path/promod3-3.4.0+ds/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target loop_pymod [ 1%] Built target scoring_pymod 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 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/extras /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/extras /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake "--color=" [ 1%] Built target sidechain_pymod [ 1%] Built target config_header make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target loop_data_dir make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 1%] Built target sidechain_data_dir cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py [ 1%] Built target scoring_data_dir cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build [ 1%] Built target init___init__.py_pymod make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend [ 1%] Built target subst_pm make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py [ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.0+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/cmake_support/substitute.cmake [ 1%] Built target core_pymod cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin/pm make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py [ 1%] Built target create_stage make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-help /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" [ 1%] Built target init_pymod cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin/pm [ 1%] Built target bash-completion cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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 -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/build make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh [ 1%] Built target promod3_scripts cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh [ 1%] Built target actions cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_afdb_modelling.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh [ 1%] Built target modelling_pymod cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh [ 1%] Built target promod3_core_headers cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.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 [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o -MF CMakeFiles/promod3_core.dir/geom_base.cc.o.d -o CMakeFiles/promod3_core.dir/geom_base.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/geom_base.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/geom_stems.cc.o -MF CMakeFiles/promod3_core.dir/geom_stems.cc.o.d -o CMakeFiles/promod3_core.dir/geom_stems.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/geom_stems.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/cluster.cc.o -MF CMakeFiles/promod3_core.dir/cluster.cc.o.d -o CMakeFiles/promod3_core.dir/cluster.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/cluster.cc [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph.cc.o -MF CMakeFiles/promod3_core.dir/graph.cc.o.d -o CMakeFiles/promod3_core.dir/graph.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/graph.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tree.cc.o -MF CMakeFiles/promod3_core.dir/tree.cc.o.d -o CMakeFiles/promod3_core.dir/tree.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/tree.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/superpose.cc.o -MF CMakeFiles/promod3_core.dir/superpose.cc.o.d -o CMakeFiles/promod3_core.dir/superpose.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/superpose.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -MF CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o.d -o CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/tetrahedral_polytope.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -MF CMakeFiles/promod3_core.dir/graph_minimizer.cc.o.d -o CMakeFiles/promod3_core.dir/graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/src/graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh [ 5%] Built target promod3_modelling_headers cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_loop_headers [ 5%] Built target promod3_scoring_headers [ 5%] Built target promod3_sidechain_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_core.so.3.4 -o ../../stage/lib64/libpromod3_core.so.3.4.0 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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_core.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4 ../../stage/lib64/libpromod3_core.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 5%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_geom.cc.o -MF CMakeFiles/_core.dir/export_geom.cc.o.d -o CMakeFiles/_core.dir/export_geom.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/pymod/export_geom.cc [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o [ 7%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 7%] 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 loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o -MF CMakeFiles/_core.dir/export_graph_minimizer.cc.o.d -o CMakeFiles/_core.dir/export_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/pymod/export_graph_minimizer.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_positions.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/all_atom_positions.cc [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o cd 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loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o -MF CMakeFiles/promod3_loop.dir/backbone.cc.o.d -o CMakeFiles/promod3_loop.dir/backbone.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/backbone.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_core_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o -MF CMakeFiles/_core.dir/wrap_core.cc.o.d -o CMakeFiles/_core.dir/wrap_core.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/pymod/wrap_core.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -MF CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o.d -o CMakeFiles/promod3_loop.dir/bb_trace_param.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/bb_trace_param.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -MF CMakeFiles/promod3_loop.dir/all_atom_env.cc.o.d -o CMakeFiles/promod3_loop.dir/all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/all_atom_env.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c 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/build/reproducible-path/promod3-3.4.0+ds/loop/src/forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o -MF CMakeFiles/promod3_loop.dir/frag_db.cc.o.d -o CMakeFiles/promod3_loop.dir/frag_db.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/frag_db.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -MF CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o.d -o CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -MF CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/mm_system_creator.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -MF CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o.d -o CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/psipred_prediction.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o -MF CMakeFiles/promod3_loop.dir/structure_db.cc.o.d -o CMakeFiles/promod3_loop.dir/structure_db.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/structure_db.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -MF CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o.d -o CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/torsion_sampler.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/sidechain_atom_rule_lookup.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/sidechain_atom_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/core/_core.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/core/_core.so CMakeFiles/_core.dir/export_geom.cc.o CMakeFiles/_core.dir/export_runtime_profiling.cc.o CMakeFiles/_core.dir/export_graph_minimizer.cc.o CMakeFiles/_core.dir/wrap_core.cc.o -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core In file included from /usr/include/c++/13/string:54, from /usr/include/boost/assert/source_location.hpp:15, from /usr/include/boost/exception/exception.hpp:9, from /usr/include/boost/throw_exception.hpp:21, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:31, from /usr/include/boost/smart_ptr/shared_ptr.hpp:18, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:22, from /build/reproducible-path/promod3-3.4.0+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>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:899:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.0+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/13/bits/basic_string.h:1079:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1079 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /usr/include/ost/generic_property.hh:34, from /usr/include/ost/mol/entity_base.hh:25, from /usr/include/ost/mol/entity_view.hh:27, from /build/reproducible-path/promod3-3.4.0+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++/13/string:42: In static member function 'static void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/13/bits/basic_string.h:428:23, 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++/13/bits/basic_string.h:877:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.0+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/13/bits/char_traits.h:358:16: 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] 358 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.0+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/13/bits/basic_string.h:900:24: 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] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2338:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2350:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2160:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/reproducible-path/promod3-3.4.0+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/13/bits/basic_string.h:900:24: 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] 900 | _M_capacity(__str._M_allocated_capacity); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 19%] Linking CXX shared library ../../stage/lib64/libpromod3_loop.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_loop.so.3.4 -o ../../stage/lib64/libpromod3_loop.so.3.4.0 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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4 ../../stage/lib64/libpromod3_loop.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make 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-I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o -MF CMakeFiles/_loop.dir/export_backbone.cc.o.d -o CMakeFiles/_loop.dir/export_backbone.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_backbone.cc [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o [ 21%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o [ 22%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/bb_dep_rotamer_lib.cc [ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_env.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_env.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_env.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_all_atom_env.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/backbone_overall_scorer.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -MF CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o.d -o CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/scoring_object_loader.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -MF CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o.d -o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_amino_acid_atoms.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o -MF CMakeFiles/_loop.dir/export_frag_db.cc.o.d -o CMakeFiles/_loop.dir/export_frag_db.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_frag_db.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o [ 25%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o [ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o -MF CMakeFiles/_loop.dir/export_fragger.cc.o.d -o CMakeFiles/_loop.dir/export_fragger.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_fragger.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -MF CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o.d -o CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/backbone_score_base.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -MF CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o.d -o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_forcefield_lookup.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -MF CMakeFiles/promod3_sidechain.dir/disulfid.cc.o.d -o CMakeFiles/promod3_sidechain.dir/disulfid.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/disulfid.cc [ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/cbeta_env_listener.cc [ 28%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -MF CMakeFiles/_loop.dir/export_loop_object_loader.cc.o.d -o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_loop_object_loader.cc [ 28%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o -MF CMakeFiles/promod3_sidechain.dir/frame.cc.o.d -o CMakeFiles/promod3_sidechain.dir/frame.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/frame.cc [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/particle_scoring.cc [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/scwrl4_particle_scoring.cc [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/scwrl3_particle_scoring.cc [ 29%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -MF CMakeFiles/_loop.dir/export_mm_system_creator.cc.o.d -o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_mm_system_creator.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/vina_particle_scoring.cc [ 32%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -MF CMakeFiles/_loop.dir/export_psipred_prediction.cc.o.d -o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_psipred_prediction.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer.cc [ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/cb_packing_score.cc [ 33%] 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CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_cruncher.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o -MF CMakeFiles/_loop.dir/export_structure_db.cc.o.d -o CMakeFiles/_loop.dir/export_structure_db.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_structure_db.cc [ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -MF CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/cbeta_score.cc [ 35%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -MF CMakeFiles/_loop.dir/export_torsion_sampler.cc.o.d -o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_torsion_sampler.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_density.cc [ 35%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/reduced_env_listener.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_group.cc [ 36%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_loop_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o -MF CMakeFiles/_loop.dir/wrap_loop.cc.o.d -o CMakeFiles/_loop.dir/wrap_loop.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/wrap_loop.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -MF CMakeFiles/promod3_scoring.dir/reduced_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/reduced_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/reduced_score.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/clash_env_listener.cc [ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_id.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/clash_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/clash_score.cc [ 40%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o -MF CMakeFiles/promod3_scoring.dir/density_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/density_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/density_score.cc [ 40%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/hbond_env_listener.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_lib.cc [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -MF CMakeFiles/promod3_scoring.dir/hbond_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/hbond_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/hbond_score.cc In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, from /usr/include/boost/python/object/class_metadata.hpp:14, from /usr/include/boost/python/class.hpp:23, from /usr/include/boost/python.hpp:18, from /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/export_helper.hh:66:16: /usr/include/boost/python/extract.hpp:185:11: warning: '*(bool*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | ); | ^ In file included from /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/export_mm_system_creator.cc:18: /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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])); | ^~~~~~~~~~~~~~~~ [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/ss_agreement_score.cc [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/ss_agreement_env_listener.cc [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_lib_entry.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/sidechain_connector.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_lib_reader.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -MF CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o.d -o CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/sidechain_object_loader.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_constructor.cc [ 46%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/rotamer_lookup.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -MF CMakeFiles/promod3_scoring.dir/torsion_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/torsion_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/torsion_score.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -MF CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/pairwise_score.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -MF CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o.d -o CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/constraint_constructor.cc [ 49%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so CMakeFiles/_loop.dir/export_all_atom_env.cc.o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o CMakeFiles/_loop.dir/export_amino_acid_atoms.cc.o CMakeFiles/_loop.dir/export_backbone.cc.o CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o CMakeFiles/_loop.dir/export_frag_db.cc.o CMakeFiles/_loop.dir/export_fragger.cc.o CMakeFiles/_loop.dir/export_loop_object_loader.cc.o CMakeFiles/_loop.dir/export_mm_system_creator.cc.o CMakeFiles/_loop.dir/export_psipred_prediction.cc.o CMakeFiles/_loop.dir/export_structure_db.cc.o CMakeFiles/_loop.dir/export_torsion_sampler.cc.o CMakeFiles/_loop.dir/wrap_loop.cc.o -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.4.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 [ 49%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/scwrl4_rotamer_constructor.cc make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 49%] Built target _loop [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/all_atom_overall_scorer.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/all_atom_interaction_env_listener.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/all_atom_interaction_score.cc [ 52%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/scwrl3_rotamer_constructor.cc [ 52%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -MF CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o.d -o CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/vina_rotamer_constructor.cc [ 52%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -MF CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o.d -o CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/subrotamer_optimizer.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -MF CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o.d -o CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/src/all_atom_clash_score.cc [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_scoring.so.3.4 -o ../../stage/lib64/libpromod3_scoring.so.3.4.0 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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 [ 54%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_sidechain.so.3.4 -o ../../stage/lib64/libpromod3_sidechain.so.3.4.0 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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.4.0 ../../stage/lib64/libpromod3_scoring.so.3.4 ../../stage/lib64/libpromod3_scoring.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 54%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o -MF CMakeFiles/_scoring.dir/export_backbone_score.cc.o.d -o CMakeFiles/_scoring.dir/export_backbone_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_backbone_score.cc [ 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_density_scorer.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o -MF CMakeFiles/_scoring.dir/export_density_scorer.cc.o.d -o CMakeFiles/_scoring.dir/export_density_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_density_scorer.cc [ 59%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -MF CMakeFiles/_scoring.dir/export_all_atom_score.cc.o.d -o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_all_atom_score.cc [ 60%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -MF CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_scwrl3_energy_functions.cc [ 60%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o -MF CMakeFiles/_scoring.dir/wrap_scoring.cc.o.d -o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/wrap_scoring.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o -MF CMakeFiles/_scoring.dir/export_object_loader.cc.o.d -o CMakeFiles/_scoring.dir/export_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_object_loader.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -MF CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o.d -o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_pairwise_functions.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_scoring_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -MF CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o.d -o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/export_constraint_constructor.cc cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.4.0 ../../stage/lib64/libpromod3_sidechain.so.3.4 ../../stage/lib64/libpromod3_sidechain.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 60%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o [ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o [ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o -MF CMakeFiles/_sidechain.dir/export_connector.cc.o.d -o CMakeFiles/_sidechain.dir/export_connector.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_connector.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer_graph.cc [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer_cruncher.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o cd /build/reproducible-path/promod3-3.4.0+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 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/build/reproducible-path/promod3-3.4.0+ds/modelling/src/backbone_relaxer.cc [ 69%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o -MF CMakeFiles/promod3_modelling.dir/ccd.cc.o.d -o CMakeFiles/promod3_modelling.dir/ccd.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/ccd.cc [ 70%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer_ids.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o -MF CMakeFiles/promod3_modelling.dir/kic.cc.o.d -o CMakeFiles/promod3_modelling.dir/kic.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/kic.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -MF CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o.d -o CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/loop_candidate.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/monte_carlo.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer_lib.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -MF CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o.d -o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_sidechain_object_loader.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_rotamer_constructor.cc [ 73%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -MF CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o.d -o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/export_subrotamer_optimizer.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/monte_carlo_closer.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/monte_carlo_cooler.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/monte_carlo_sampler.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -MF CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o.d -o CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/monte_carlo_scorer.cc [ 77%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_sidechain_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -MF CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o.d -o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/wrap_sidechain.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -MF CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o.d -o CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/rigid_blocks.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o -MF CMakeFiles/promod3_modelling.dir/score_container.cc.o.d -o CMakeFiles/promod3_modelling.dir/score_container.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/score_container.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -MF CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o.d -o CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/scoring_weights.cc [ 80%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -MF CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o.d -o CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -MF CMakeFiles/promod3_modelling.dir/motif_finder.cc.o.d -o CMakeFiles/promod3_modelling.dir/motif_finder.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/motif_finder.cc [ 81%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/afdb.cc.o -MF CMakeFiles/promod3_modelling.dir/afdb.cc.o.d -o CMakeFiles/promod3_modelling.dir/afdb.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/src/afdb.cc [ 81%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/scoring/_scoring.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/scoring/_scoring.so CMakeFiles/_scoring.dir/export_backbone_score.cc.o CMakeFiles/_scoring.dir/export_all_atom_score.cc.o CMakeFiles/_scoring.dir/export_object_loader.cc.o CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o CMakeFiles/_scoring.dir/export_density_scorer.cc.o CMakeFiles/_scoring.dir/wrap_scoring.cc.o -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.4.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/reproducible-path/promod3-3.4.0+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/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so CMakeFiles/_sidechain.dir/export_connector.cc.o CMakeFiles/_sidechain.dir/export_disulfid.cc.o CMakeFiles/_sidechain.dir/export_frame.cc.o CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o CMakeFiles/_sidechain.dir/export_particle.cc.o CMakeFiles/_sidechain.dir/export_rotamer.cc.o CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.4.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libpromod3_modelling.so.3.4 -o ../../stage/lib64/libpromod3_modelling.so.3.4.0 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/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so ../../stage/lib64/libpromod3_scoring.so.3.4.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_modelling.so.3.4.0 ../../stage/lib64/libpromod3_modelling.so.3.4 ../../stage/lib64/libpromod3_modelling.so make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 81%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod 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modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o -MF CMakeFiles/_modelling.dir/export_gap.cc.o.d -o CMakeFiles/_modelling.dir/export_gap.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/export_gap.cc cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -MF CMakeFiles/_modelling.dir/export_extension_scheme.cc.o.d -o CMakeFiles/_modelling.dir/export_extension_scheme.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/export_extension_scheme.cc [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_afdb.cc.o -MF CMakeFiles/_modelling.dir/export_afdb.cc.o.d -o CMakeFiles/_modelling.dir/export_afdb.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/export_afdb.cc [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o cd /build/reproducible-path/promod3-3.4.0+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 -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -D_modelling_EXPORTS -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o -MF CMakeFiles/_modelling.dir/wrap_modelling.cc.o.d -o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/wrap_modelling.cc [ 90%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/modelling/_modelling.so cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../stage/lib64/python3.11/site-packages/promod3/modelling/_modelling.so CMakeFiles/_modelling.dir/export_extension_scheme.cc.o CMakeFiles/_modelling.dir/export_gap.cc.o CMakeFiles/_modelling.dir/export_gap_extender.cc.o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o CMakeFiles/_modelling.dir/export_loop_closure.cc.o CMakeFiles/_modelling.dir/export_model.cc.o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o CMakeFiles/_modelling.dir/export_score_container.cc.o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o CMakeFiles/_modelling.dir/export_motif_finder.cc.o CMakeFiles/_modelling.dir/export_afdb.cc.o CMakeFiles/_modelling.dir/wrap_modelling.cc.o -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_modelling.so.3.4.0 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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 -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake "--color=" make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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 -f scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake "--color=" make -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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 -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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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 -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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 [ 91%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_torsion_sampler.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup [ 92%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 92%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 94%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_structure_db.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer [ 95%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer [ 95%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [ 95%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat [ 97%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/loop/data/portable_frag_db.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer [ 98%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer 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. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] Built target generate_scoring_data_aa_packing_scorer.dat [ 98%] Built target generate_scoring_data_cb_packing_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[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/depend cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/DependInfo.cmake "--color=" [ 98%] Built target generate_scoring_data_cbeta_scorer.dat [ 98%] Built target generate_scoring_data_hbond_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 [ 98%] Built target generate_loop_data_ff_lookup_charmm.dat make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/DependInfo.cmake "--color=" make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make -f sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+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[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat [ 98%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/convert_binaries.py'\ '/build/reproducible-path/promod3-3.4.0+ds/scoring/data/portable_aa_scorer.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.0+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/reproducible-path/promod3-3.4.0+ds/sidechain/data/convert_lib.py'\ '/build/reproducible-path/promod3-3.4.0+ds/sidechain/data/portable_lib.dat'\ '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib [100%] Built target generate_scoring_data_reduced_scorer.dat Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. Compound library not available. Some functionality may not work as expected. make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_extended.dat [100%] Built target generate_loop_data_torsion_sampler.dat [100%] Built target generate_loop_data_torsion_sampler_coil.dat [100%] Built target generate_loop_data_torsion_sampler_helical.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_torsion_scorer.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_ss_agreement_scorer.dat [100%] Built target generate_sidechain_data_lib.dat [100%] Built target generate_scoring_data_aa_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_bb_dep_lib.dat make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/depend make[3]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.0+ds -B/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.0+ds -B/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[4]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-model /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-rawmodel /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-help /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/pm-build-sidechains /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/actions/tests/data/seq_ins.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 1%] running checks test_actions.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests//test_helper.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/broken_on_purpose.chemlib /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/1crn.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2jlp-1.json /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/1crn.hhm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/alignment.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake_1.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake_2trg.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake_3.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake.fas.gz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake_nel.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/tests/data/fasta/1ake_sw.fas /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./check_io.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./cluster.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./dynamic_spatial_organizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./export_helper.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./geom_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./geom_stems.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./message.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_data_sink.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_data_source.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./portable_binary_serializer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./runtime_profiling.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./superpose.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./enumerator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./graph.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./tree.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./tetrahedral_polytope.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./graph_minimizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/src/./eigen_types.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/config/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o -MF CMakeFiles/test_suite_core.dir/test_check_io.cc.o.d -o CMakeFiles/test_suite_core.dir/test_check_io.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -MF CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o.d -o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -MF CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o.d -o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o -MF CMakeFiles/test_suite_core.dir/tests.cc.o.d -o CMakeFiles/test_suite_core.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/core/tests/tests.cc [ 6%] Linking CXX executable ../../tests/core/test_suite_core cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_core.dir/test_check_io.cc.o CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o CMakeFiles/test_suite_core.dir/tests.cc.o -o ../../tests/core/test_suite_core -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/__init__.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/helper.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/core/pymod/pm3argparse.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 9%] running checks for module core cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 10%] running checks test_setcompoundschemlib.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/core/tests/test_setcompoundschemlib.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.130s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 11%] running checks test_pm3argparse.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/core/tests/test_pm3argparse.py" Compound library not available. Some functionality may not work as expected. .................................................................. ---------------------------------------------------------------------- Ran 66 tests in 1.531s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_closegaps.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_molprobity.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_pipeline.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_ring_punches.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_denovo.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_fragger_handle.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_reconstruct_sidechains.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_monte_carlo.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_mhandle_helper.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_alignment_fiddling.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_raw_model.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_planar_rings.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_planar_rings.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod/_afdb_modelling.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_afdb_modelling.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./all_atom_env.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./all_atom_positions.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./amino_acid_atoms.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./backbone.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./bb_trace_param.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./data_bag.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_hash_table.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./dense_map.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./density_creator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./forcefield_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./frag_db.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./fragger.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./hydrogen_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./hydrogen_rule_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./idx_handler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./loop_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./mm_system_creator.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./psipred_prediction.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./stem_geom.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./structure_db.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./torsion_sampler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./ushort_vec.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./sidechain_atom_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/src/./structure_db_custom_types.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./backbone_score_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./backbone_overall_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./scoring_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cbeta_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cb_packing_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./cbeta_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./reduced_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./reduced_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./clash_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./clash_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./density_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./hbond_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./hbond_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./ss_agreement_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./ss_agreement_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./torsion_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./pairwise_scoring_function.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./pairwise_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./constraint_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_score_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_overall_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_interaction_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_packing_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./all_atom_clash_score.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/src/./scwrl3_energy_functions.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./disulfid.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./frame.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_graph.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle_scoring_base.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./vina_particle_scoring.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_cruncher.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_density.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_group.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_id.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib_entry.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lib_reader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./sidechain_connector.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./sidechain_object_loader.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./rotamer_lookup.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./vina_rotamer_constructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/src/./subrotamer_optimizer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod/__init__.py /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./extension_scheme.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./gap.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./gap_extender.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./model.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./all_atom_relaxer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./backbone_relaxer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./ccd.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./kic.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./loop_candidate.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_closer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_cooler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_sampler.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./monte_carlo_scorer.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./rigid_blocks.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./score_container.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./scoring_weights.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./sidechain_reconstructor.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./sidechain_env_listener.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./motif_finder.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./robin_hood.h /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/src/./afdb.hh /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./afdb.hh make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/1A88A.hhm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/1A88A.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/1A88A_with_gap.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/1akyA.horiz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/all_aa.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/all_aa_prot_ref.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/loop/tests/data/CHARMM27.dat /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 77%] Built target test_data_loop make -f 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loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o cd /build/reproducible-path/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c 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-ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o -MF CMakeFiles/test_suite_loop.dir/tests.cc.o.d -o CMakeFiles/test_suite_loop.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/loop/tests/tests.cc [ 84%] Linking CXX executable ../../tests/loop/test_suite_loop cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_suite_loop.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o CMakeFiles/test_suite_loop.dir/tests.cc.o -o ../../tests/loop/test_suite_loop -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/loop/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 84%] running checks for module loop cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/tests/data/1CRNA.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/tests/data/3DEFA.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/scoring/tests/data/clash_test.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -MF CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o.d -o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/tests/test_all_atom_scorer.cc /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o -MF CMakeFiles/test_suite_scoring.dir/tests.cc.o.d -o CMakeFiles/test_suite_scoring.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/scoring/tests/tests.cc [ 89%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o CMakeFiles/test_suite_scoring.dir/tests.cc.o -o ../../tests/scoring/test_suite_scoring -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_scoring.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 90%] running checks for module scoring cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/sidechain cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests/data/all_sc.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make 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-MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests/test_rotamers.cc [ 92%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o cd /build/reproducible-path/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o -MF CMakeFiles/test_suite_sidechain.dir/tests.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests/tests.cc [ 93%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o CMakeFiles/test_suite_sidechain.dir/tests.cc.o -o ../../tests/sidechain/test_suite_sidechain -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 93%] running checks for module sidechain cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1cjx-1.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1cjx-1.pdb.gz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1CRN.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_build.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_final.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_rec.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_sc.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1crn_sc_test.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1CRNA.hhm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1eye.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1eye_rec.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1eye_sc_test.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/1mcg.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2aoh-1_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2dbs.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2jlp-1.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2jlp-1.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2xim-1.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/2xim-1.pdb.gz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/3b08-3.pdb.gz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/3b08-3.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/4nyk.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/4ksl-1.pdb.gz /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/4ksl-1.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/5d52-1.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/5d52-1_cut.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/CA-3cm91E.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/CA-3cm91E.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/cbeta.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/cbeta.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/del.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/ff_NAD.dat /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/gly.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/gly_on_top.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/gly_almost_on_top.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/gly_shifted_nter.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/hetero-punched.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/ins.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/neighbor-punched.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/port_frag_db.dat /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/port_str_db.dat /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/sep.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/sep.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/seq.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/smtl2bl4.1.pdb /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/ter.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/data/double_gap_aln.fasta /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -MF CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o.d -o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o -c /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_NO_LIB -I/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o -MF CMakeFiles/test_suite_modelling.dir/tests.cc.o.d -o CMakeFiles/test_suite_modelling.dir/tests.cc.o -c /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/tests.cc [ 95%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o CMakeFiles/test_suite_modelling.dir/tests.cc.o -o ../../tests/modelling/test_suite_modelling -L/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.83.0 ../../stage/lib64/libpromod3_modelling.so.3.4.0 ../../stage/lib64/libpromod3_scoring.so.3.4.0 ../../stage/lib64/libpromod3_sidechain.so.3.4.0 ../../stage/lib64/libpromod3_loop.so.3.4.0 ../../stage/lib64/libpromod3_core.so.3.4.0 /usr/lib/x86_64-linux-gnu/libost_io.so /usr/lib/x86_64-linux-gnu/libost_mol.so /usr/lib/x86_64-linux-gnu/libost_seq.so /usr/lib/x86_64-linux-gnu/libost_seq_alg.so /usr/lib/x86_64-linux-gnu/libost_mol_alg.so /usr/lib/x86_64-linux-gnu/libost_conop.so /usr/lib/x86_64-linux-gnu/libost_img.so /usr/lib/x86_64-linux-gnu/libost_mol_mm.so /usr/lib/x86_64-linux-gnu/libost_base.so /usr/lib/x86_64-linux-gnu/libost_geom.so /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks for module modelling cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_close_gaps.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/test_close_gaps.py" Compound library not available. Some functionality may not work as expected. ................................. ---------------------------------------------------------------------- Ran 33 tests in 19.724s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 96%] running checks test_gap_extension.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/test_gap_extension.py" Compound library not available. Some functionality may not work as expected. ...... ---------------------------------------------------------------------- Ran 6 tests in 0.016s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_modelling.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+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 0.078s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_pipeline.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+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 37.065s OK OpenMM CPU platform not available. Skipping almost_on_top check. phenix.molprobity is missing. Please install it and make it available in your PATH to execute test testMolProbity. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 97%] running checks test_ring_punches.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/test_ring_punches.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.119s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_sidechain_reconstruction.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/test_sidechain_reconstruction.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 2.216s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/modelling/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/modelling/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_alignment_fiddling.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/modelling/tests/test_alignment_fiddling.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.010s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/promod3-3.4.0+ds/scripts/pm.in -DOUT_FILE=pm -DOST_ROOT="/usr" -DLIBDIR=lib64 -DLIBEXECPATH=libexec/promod3 -DPYTHON_MODULE_PATH=python3.11/site-packages/ -DOST_PYMOD_PATH=/usr/lib/python3/dist-packages -DPython_EXECUTABLE=/usr/bin/python3 -P /build/reproducible-path/promod3-3.4.0+ds/cmake_support/substitute.cmake make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/scripts/pm /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/bin/pm make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-model.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/actions/tests/test_action_build-model.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 4.739s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [ 98%] running checks test_action_build-rawmodel.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/actions/tests/test_action_build-rawmodel.py" Compound library not available. Some functionality may not work as expected. ... ---------------------------------------------------------------------- Ran 3 tests in 2.064s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/actions/tests /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/actions/tests /build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] running checks test_action_help.py cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/reproducible-path/promod3-3.4.0+ds/actions/tests/test_action_help.py" Compound library not available. Some functionality may not work as expected. .. ---------------------------------------------------------------------- Ran 2 tests in 0.040s OK make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[5]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/promod3-3.4.0\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/promod3-3.4.0+ds -B/build/reproducible-path/promod3-3.4.0+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/promod3-3.4.0+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.0 -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.4.0" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_core.so -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./check_io.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./cluster.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./dynamic_spatial_organizer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./export_helper.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./geom_base.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./geom_stems.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./message.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_sink.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_source.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./portable_binary_serializer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./runtime_profiling.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./superpose.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./enumerator.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./graph.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./tree.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./tetrahedral_polytope.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./graph_minimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/core/./eigen_types.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/_core.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/_core.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/helper.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/pm3argparse.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.0 -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.4.0" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_loop.so -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./all_atom_env.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./all_atom_positions.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./amino_acid_atoms.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./backbone.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./bb_trace_param.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./data_bag.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./dense_hash_table.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Up-to-date: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./density_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./forcefield_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./frag_db.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./fragger.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./idx_handler.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./loop_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./mm_system_creator.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./psipred_prediction.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./stem_geom.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./structure_db.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./torsion_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./ushort_vec.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_rule_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/loop/./structure_db_custom_types.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/_loop.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.0 -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.4.0" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_scoring.so -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./backbone_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./backbone_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./scoring_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./cb_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./reduced_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./reduced_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./clash_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./density_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./hbond_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./hbond_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./torsion_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_scoring_function.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./constraint_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_score_base.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_overall_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_packing_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_clash_score.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/scoring/./scwrl3_energy_functions.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/_scoring.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.0 -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.4.0" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./disulfid.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./frame.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_graph.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./particle.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring_base.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./vina_particle_scoring.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_cruncher.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_density.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_group.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_id.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_entry.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_reader.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_connector.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_object_loader.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lookup.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./vina_rotamer_constructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/sidechain/./subrotamer_optimizer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.0 -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.4.0" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/libpromod3_modelling.so -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./extension_scheme.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./gap.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./gap_extender.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./model.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./all_atom_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./backbone_relaxer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./ccd.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./kic.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./loop_candidate.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_closer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_cooler.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_sampler.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_scorer.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./rigid_blocks.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./score_container.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./scoring_weights.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_reconstructor.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_env_listener.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./motif_finder.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./robin_hood.h -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/include/promod3/modelling/./afdb.hh -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_modelling.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/__init__.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_denovo.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_planar_rings.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_afdb_modelling.py -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/bin/pm -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/reproducible-path/promod3-3.4.0+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds/obj-x86_64-linux-gnu' debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+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/lib64/libpromod3_${PKG}.so usr/lib/x86_64-linux-gnu; \ dh_install -p libpromod3-${PKG}3.4 usr/lib64/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/promod3-3.4.0+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib64 make[1]: Leaving directory '/build/reproducible-path/promod3-3.4.0+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:418: renaming _modelling.so to _modelling.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:418: renaming _loop.so to _loop.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:418: renaming _scoring.so to _scoring.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:418: renaming _core.so to _core.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:418: renaming _sidechain.so to _sidechain.cpython-311-x86_64-linux-gnu.so dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package promod3: substitution variable ${python3:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4-dbgsym' in '../libpromod3-core3.4-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4' in '../libpromod3-loop3.4_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4-dbgsym' in '../libpromod3-modelling3.4-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4' in '../libpromod3-scoring3.4_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4-dbgsym' in '../libpromod3-sidechain3.4-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.4.0+ds-1_all.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.4' in '../libpromod3-sidechain3.4_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.4' in '../libpromod3-core3.4_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.4' in '../libpromod3-modelling3.4_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.4-dbgsym' in '../libpromod3-scoring3.4-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.4-dbgsym' in '../libpromod3-loop3.4-dbgsym_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.4.0+ds-1_all.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.4.0+ds-1_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.4.0+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.4.0+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.4.0+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/3810101 and its subdirectories I: Current time: Wed Jul 2 20:38:03 -12 2025 I: pbuilder-time-stamp: 1751531883 Fri May 31 02:15:09 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Fri May 31 02:15:09 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Fri May 31 02:27:25 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Fri May 31 02:27:26 UTC 2024 I: promod3_3.4.0+ds-1_amd64.changes: Format: 1.8 Date: Thu, 25 Jan 2024 02:33:54 -0500 Source: promod3 Binary: libpromod3-core-dev libpromod3-core3.4 libpromod3-core3.4-dbgsym libpromod3-loop-dev libpromod3-loop3.4 libpromod3-loop3.4-dbgsym libpromod3-modelling-dev libpromod3-modelling3.4 libpromod3-modelling3.4-dbgsym libpromod3-scoring-dev libpromod3-scoring3.4 libpromod3-scoring3.4-dbgsym libpromod3-sidechain-dev libpromod3-sidechain3.4 libpromod3-sidechain3.4-dbgsym promod3 promod3-data python3-promod3 python3-promod3-dbgsym Architecture: amd64 all Version: 3.4.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libpromod3-core-dev - protein homology modelling engine libpromod3-core3.4 - protein homology modelling engine libpromod3-loop-dev - protein homology modelling engine libpromod3-loop3.4 - protein homology modelling engine libpromod3-modelling-dev - protein homology modelling engine libpromod3-modelling3.4 - protein homology modelling engine libpromod3-scoring-dev - protein homology modelling engine libpromod3-scoring3.4 - protein homology modelling engine libpromod3-sidechain-dev - protein homology modelling engine libpromod3-sidechain3.4 - protein homology modelling engine promod3 - protein homology modelling engine promod3-data - protein homology modelling engine - data files python3-promod3 - protein homology modelling engine - Python 3 package Changes: promod3 (3.4.0+ds-1) unstable; urgency=medium . * Upload to unstable. Checksums-Sha1: 8db740c2f55ab4cbe909a80978e149af75006cd8 24312 libpromod3-core-dev_3.4.0+ds-1_amd64.deb b968c6000b197ed01da82123bb0006f5b2161ace 2581516 libpromod3-core3.4-dbgsym_3.4.0+ds-1_amd64.deb 75be599c417e4406084d557218f19fb0f60858cc 93836 libpromod3-core3.4_3.4.0+ds-1_amd64.deb b457659f2c164d840083f105ae5547d8c77788f8 35348 libpromod3-loop-dev_3.4.0+ds-1_amd64.deb 8102f7c46d5fddc9de2b095de0e67111de168e7a 5282636 libpromod3-loop3.4-dbgsym_3.4.0+ds-1_amd64.deb 8373bae717d2b19cf7f2b0c1954063d99ed2ec8c 284936 libpromod3-loop3.4_3.4.0+ds-1_amd64.deb 0d3836d0ed49c4483ae67118046e60923b3e59dd 36968 libpromod3-modelling-dev_3.4.0+ds-1_amd64.deb 176fd92f87cc36d920c122814b129c13425aee03 11783708 libpromod3-modelling3.4-dbgsym_3.4.0+ds-1_amd64.deb db9337a4a3c19832a29b3ec0ee12d88bcabd4e12 307992 libpromod3-modelling3.4_3.4.0+ds-1_amd64.deb d5eb1d6f3bf427817f8e01ae01392e06f5930ef9 17920 libpromod3-scoring-dev_3.4.0+ds-1_amd64.deb 4fa80f3d526e285537064120ac471c027aba81fe 4527728 libpromod3-scoring3.4-dbgsym_3.4.0+ds-1_amd64.deb f56e4ee3a1a2bd363d7c960356455dc42483974b 178512 libpromod3-scoring3.4_3.4.0+ds-1_amd64.deb a7b10cc10a187d62c79798cebb5c5e0601daf722 19256 libpromod3-sidechain-dev_3.4.0+ds-1_amd64.deb 3ba71aed3d28b94aa498ee57c81309a6acfd02ed 4410668 libpromod3-sidechain3.4-dbgsym_3.4.0+ds-1_amd64.deb bd480b8c5c5a7c0cbc8a788f9a1f036a44e3a35d 233632 libpromod3-sidechain3.4_3.4.0+ds-1_amd64.deb 3bcd91823d69bc70ed97f710d3c04a6b8d721968 371360720 promod3-data_3.4.0+ds-1_all.deb 70e2dc837686c41676f650fd5b3161dcdbe286aa 10872 promod3_3.4.0+ds-1_all.deb 0773438bd109f0bd1e04f1c6316b5b0370d556e7 19188 promod3_3.4.0+ds-1_amd64.buildinfo 5e7c67194564043ca84b63283b2a83696d3cfab6 19106612 python3-promod3-dbgsym_3.4.0+ds-1_amd64.deb 5b1420b2cc21bba29870007235a6ab672f117ced 1054416 python3-promod3_3.4.0+ds-1_amd64.deb Checksums-Sha256: 592a37f5dc3236a2134dc992d08c2429c5684d1c9e32764d3d2d4f51e7c30b63 24312 libpromod3-core-dev_3.4.0+ds-1_amd64.deb 2bbd30d93aab3d0d3d3285279bbcfc6458208ab81d969e50085921579751f5c9 2581516 libpromod3-core3.4-dbgsym_3.4.0+ds-1_amd64.deb 88b52c9b58b10faae4494f4dfec29e282ca97cf25536b0b91426b5f9ae704acd 93836 libpromod3-core3.4_3.4.0+ds-1_amd64.deb bbadf0c2a824bc794d7ba1037505a15913fc73ac43831566a4510c38feae90a4 35348 libpromod3-loop-dev_3.4.0+ds-1_amd64.deb 2429ea5e1e2a6d24fdc6946abc2b1ad4572c9dbb16e546eeff5b75a036f52140 5282636 libpromod3-loop3.4-dbgsym_3.4.0+ds-1_amd64.deb 706c0c9468411d0d5ca6c44eb1bf1af1a327693e74496adfc86d8d6c2b0d1c5e 284936 libpromod3-loop3.4_3.4.0+ds-1_amd64.deb 772d36cd9f7182cc37f3c28242c3895663b02ac0bbe96996acfc4e18c096ecb6 36968 libpromod3-modelling-dev_3.4.0+ds-1_amd64.deb 04cba9621624a6fc05f39ef632dbd88ca0cac60e9fe8ced294d01cb1305f465e 11783708 libpromod3-modelling3.4-dbgsym_3.4.0+ds-1_amd64.deb 8e51a8ee190ecdb4ef6cacaa9aec754463de0d35f2dac67ad20ab1790294e38d 307992 libpromod3-modelling3.4_3.4.0+ds-1_amd64.deb 6972cd33cab1ede58bbe7dec6979abc2030d95e47cdbc967b11df0ab4cbaf12a 17920 libpromod3-scoring-dev_3.4.0+ds-1_amd64.deb 683ea043648b42186af0df80c72c4d494b9206de2e06680cf85b244411516367 4527728 libpromod3-scoring3.4-dbgsym_3.4.0+ds-1_amd64.deb cfcefd2c5756b5c7ea2b0c7a09c81a7a8db97748b9a77736116108a9cc8bf873 178512 libpromod3-scoring3.4_3.4.0+ds-1_amd64.deb 433f8102e04d1fc31861ac4eea704f49e3ce479b04d7d98702f93f2b919d1908 19256 libpromod3-sidechain-dev_3.4.0+ds-1_amd64.deb cc2e1271d965cf009038e155c175e0574402aec2c203fe562d286abc8c317087 4410668 libpromod3-sidechain3.4-dbgsym_3.4.0+ds-1_amd64.deb 4434337259cdb6c436645581998efb4c52ec388641102c7eef816a5ff2efe676 233632 libpromod3-sidechain3.4_3.4.0+ds-1_amd64.deb e520327a8f9db40a591a8f18c9efa1cb5f2fccfe39d88b9e55a75a987a15cdbd 371360720 promod3-data_3.4.0+ds-1_all.deb c356ed5dc240d0dba27a04db2b1dc8defdae814415ff6c4e486c319474218655 10872 promod3_3.4.0+ds-1_all.deb 2dc573896e1698069c1dce84130232cc6d37a1f9a9ffe8e42e69fe5ebb1c9340 19188 promod3_3.4.0+ds-1_amd64.buildinfo 7e45f1e736ca2991d1cb911fe942d2bf800feca1685333f0c9d08cac69ed0dce 19106612 python3-promod3-dbgsym_3.4.0+ds-1_amd64.deb fcc45d6a317d6053532db5e920a8971fc51dd2f7ba932fd507c0215f74def759 1054416 python3-promod3_3.4.0+ds-1_amd64.deb Files: 126a7159ad412c5ddbcfaee9095788ab 24312 libdevel optional libpromod3-core-dev_3.4.0+ds-1_amd64.deb a04fb77ce71c2b0bc7eee03d3c0b8b1e 2581516 debug optional libpromod3-core3.4-dbgsym_3.4.0+ds-1_amd64.deb ca0e5637efb3ade27dad2f2c7a3fdf2b 93836 libs optional libpromod3-core3.4_3.4.0+ds-1_amd64.deb 783c3c5c2aadc3ed09b072fec2d3c0d7 35348 libdevel optional libpromod3-loop-dev_3.4.0+ds-1_amd64.deb 01189b1fa11a09e57ebedac8cd97e6c7 5282636 debug optional libpromod3-loop3.4-dbgsym_3.4.0+ds-1_amd64.deb ea1599e546e2d4a8424fb5aff8cb1c51 284936 libs optional libpromod3-loop3.4_3.4.0+ds-1_amd64.deb 99a56cc1e312e941c7363400f206bff8 36968 libdevel optional libpromod3-modelling-dev_3.4.0+ds-1_amd64.deb 17d41b6d0064e741a986203192166af4 11783708 debug optional libpromod3-modelling3.4-dbgsym_3.4.0+ds-1_amd64.deb 2e0635bbb39524355edfaaa971d29bd1 307992 libs optional libpromod3-modelling3.4_3.4.0+ds-1_amd64.deb d36a0206f0b060c8a867bfd441eff3b6 17920 libdevel optional libpromod3-scoring-dev_3.4.0+ds-1_amd64.deb 2975a1211640c1df1d8c6d036450f108 4527728 debug optional libpromod3-scoring3.4-dbgsym_3.4.0+ds-1_amd64.deb 87952a7c05429c06bc4f7533e9ff26ed 178512 libs optional libpromod3-scoring3.4_3.4.0+ds-1_amd64.deb ec5bfa8b9c71b72c1c56d543bfba3937 19256 libdevel optional libpromod3-sidechain-dev_3.4.0+ds-1_amd64.deb 359feea0ce24c8c0e7538310a23ba2a1 4410668 debug optional libpromod3-sidechain3.4-dbgsym_3.4.0+ds-1_amd64.deb 776a70fdbf4a983bab28a64250b9a214 233632 libs optional libpromod3-sidechain3.4_3.4.0+ds-1_amd64.deb f80b95a7553f6c6123d668f2ebbff12e 371360720 science optional promod3-data_3.4.0+ds-1_all.deb c5a71da8534d3d94550a3a0ab0abb16f 10872 science optional promod3_3.4.0+ds-1_all.deb 635a6337f40c64f72274e86754ba5bcf 19188 science optional promod3_3.4.0+ds-1_amd64.buildinfo f9b78a1c80e67ac09fad0ac16025b3e2 19106612 debug optional python3-promod3-dbgsym_3.4.0+ds-1_amd64.deb 504802c3c1c5f5fdc476bc03c9522aa2 1054416 python optional python3-promod3_3.4.0+ds-1_amd64.deb Fri May 31 02:27:27 UTC 2024 I: diffoscope 268 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-14526.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/promod3_3.4.0+ds-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/promod3_3.4.0+ds-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/promod3_3.4.0+ds-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/b1/promod3_3.4.0+ds-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.FTYUhzZi/b2/promod3_3.4.0+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 abc.DotChangesFile ## main (total time: 5.056s) 5.056s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 4.646s) 4.646s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5.409s CPU time consumed: 5.408s Fri May 31 02:27:33 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Fri May 31 02:27:33 UTC 2024 I: promod3 from unstable built successfully and reproducibly on amd64. Fri May 31 02:27:35 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 31 02:27:35 UTC 2024 I: Submitting 20K b1/promod3_3.4.0+ds-1_amd64.buildinfo.asc Fri May 31 02:27:38 UTC 2024 I: Submitting 20K b2/promod3_3.4.0+ds-1_amd64.buildinfo.asc Fri May 31 02:27:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 31 02:27:41 UTC 2024 I: Done submitting .buildinfo files. Fri May 31 02:27:41 UTC 2024 I: Removing signed promod3_3.4.0+ds-1_amd64.buildinfo.asc files: removed './b1/promod3_3.4.0+ds-1_amd64.buildinfo.asc' removed './b2/promod3_3.4.0+ds-1_amd64.buildinfo.asc'