I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 6 03:42:34 +14 2023 I: pbuilder-time-stamp: 1685972554 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [promod3_3.2.1+ds-6.dsc] I: copying [./promod3_3.2.1+ds.orig.tar.xz] I: copying [./promod3_3.2.1+ds-6.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 22 22:20:26 2022 +14 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_3.2.1+ds-6.dsc: no acceptable signature found dpkg-source: info: extracting promod3 in promod3-3.2.1+ds dpkg-source: info: unpacking promod3_3.2.1+ds.orig.tar.xz dpkg-source: info: unpacking promod3_3.2.1+ds-6.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 PM3ArgParseTests.patch dpkg-source: info: applying 7102f98564702dad9903dc77c6c5a940ea8f7777.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/3094074/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 6 03:43 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3094074/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3094074/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=8b386341f8da42ffa83a31cfa049a8a0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3094074 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.EpZkSHqo/pbuilderrc_aZRT --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EpZkSHqo/b2 --logfile b2/build.log --extrapackages usrmerge promod3_3.2.1+ds-6.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Jun 6 03:43 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3094074/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 (>= 2.3.1-6), 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 ... 19591 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 (>= 2.3.1-6); 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-lyx{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libboost-dev{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-python-dev{a} libboost-python1.74-dev{a} libboost-python1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-test-dev{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost-thread1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcups2{a} libcurl4{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} libelf1{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} libglib2.0-0{a} libglu1-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{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} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm15{a} libmagic-mgc{a} libmagic1{a} libmd4c0{a} libmtdev1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopengl0{a} libopenjp2-7{a} libopenmm7.7{a} libost-base-dev{a} libost-base2.3{a} libost-bindings2.3{a} libost-conop-dev{a} libost-conop2.3{a} libost-db2.3{a} libost-geom-dev{a} libost-geom2.3{a} libost-gfx2.3{a} libost-gui2.3{a} libost-img-alg2.3{a} libost-img-dev{a} libost-img2.3{a} libost-info-dev{a} libost-info2.3{a} libost-io-dev{a} libost-io2.3{a} libost-mol-alg-dev{a} libost-mol-alg2.3{a} libost-mol-dev{a} libost-mol-mm-dev{a} libost-mol-mm2.3{a} libost-mol2.3{a} libost-seq-alg-dev{a} libost-seq-alg2.3{a} libost-seq-dev{a} libost-seq2.3{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libqt5core5a{a} libqt5dbus5{a} libqt5designer5{a} libqt5gui5{a} libqt5help5{a} libqt5network5{a} libqt5printsupport5{a} libqt5sql5{a} libqt5test5{a} libqt5widgets5{a} libqt5xml5{a} libraqm0{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1{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} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} openstructure{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-ost{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-pythran{a} python3-scipy{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tk8.6-blt2.5{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 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 psmisc publicsuffix python3-bs4 python3-html5lib python3-olefile qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xdg-user-dirs 0 packages upgraded, 296 newly installed, 0 to remove and 0 not upgraded. Need to get 301 MB of archives. After unpacking 1178 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.6-1 [200 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74.0 amd64 1.74.0+ds1-21 [218 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74-dev amd64 1.74.0+ds1-21 [219 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74-dev amd64 1.74.0+ds1-21 [279 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem-dev amd64 1.74.0.3 [4368 B] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-21 [487 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-21 [557 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-21 [248 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-21 [357 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74.0 amd64 1.74.0+ds1-21 [289 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get: 111 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74-dev amd64 1.74.0+ds1-21 [310 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libboost-python-dev amd64 1.74.0.3 [4632 B] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74.0 amd64 1.74.0+ds1-21 [453 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74-dev amd64 1.74.0+ds1-21 [526 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libboost-test-dev amd64 1.74.0.3 [4368 B] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3 [244 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libdouble-conversion3 amd64 3.2.1-1 [41.5 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libgbm1 amd64 22.3.6-1+deb12u1 [38.0 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2 [192 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 145 http://deb.debian.org/debian bookworm/main amd64 libegl-mesa0 amd64 22.3.6-1+deb12u1 [114 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 libevdev2 amd64 1.13.0+dfsg-1 [34.0 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 libfftw3-single3 amd64 3.3.10-1 [806 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get: 157 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get: 159 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get: 162 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 libopengl0 amd64 1.6.0-1 [30.6 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 libgudev-1.0-0 amd64 237-2 [15.1 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 176 http://deb.debian.org/debian bookworm/main amd64 libwacom-common all 2.6.0-1 [58.4 kB] Get: 177 http://deb.debian.org/debian bookworm/main amd64 libwacom9 amd64 2.6.0-1 [21.5 kB] Get: 178 http://deb.debian.org/debian bookworm/main amd64 libinput-bin amd64 1.22.1-1 [23.2 kB] Get: 179 http://deb.debian.org/debian bookworm/main amd64 libmtdev1 amd64 1.1.6-1 [23.0 kB] Get: 180 http://deb.debian.org/debian bookworm/main amd64 libinput10 amd64 1.22.1-1 [125 kB] Get: 181 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 182 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 183 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 184 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get: 185 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 186 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get: 187 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 188 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 189 http://deb.debian.org/debian bookworm/main amd64 libmd4c0 amd64 0.4.8-1 [44.2 kB] Get: 190 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get: 191 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get: 192 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get: 193 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get: 194 http://deb.debian.org/debian bookworm/main amd64 libopenmm7.7 amd64 7.7.0+dfsg-9+b1 [856 kB] Get: 195 http://deb.debian.org/debian bookworm/main amd64 libost-base2.3 amd64 2.3.1-9 [32.6 kB] Get: 196 http://deb.debian.org/debian bookworm/main amd64 libost-base-dev amd64 2.3.1-9 [24.1 kB] Get: 197 http://deb.debian.org/debian bookworm/main amd64 libost-geom2.3 amd64 2.3.1-9 [64.0 kB] Get: 198 http://deb.debian.org/debian bookworm/main amd64 libost-mol2.3 amd64 2.3.1-9 [335 kB] Get: 199 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get: 200 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get: 201 http://deb.debian.org/debian bookworm/main amd64 libqt5core5a amd64 5.15.8+dfsg-11 [1809 kB] Get: 202 http://deb.debian.org/debian bookworm/main amd64 libqt5xml5 amd64 5.15.8+dfsg-11 [122 kB] Get: 203 http://deb.debian.org/debian bookworm/main amd64 libost-info2.3 amd64 2.3.1-9 [112 kB] Get: 204 http://deb.debian.org/debian bookworm/main amd64 libost-seq2.3 amd64 2.3.1-9 [87.6 kB] Get: 205 http://deb.debian.org/debian bookworm/main amd64 libost-bindings2.3 amd64 2.3.1-9 [85.0 kB] Get: 206 http://deb.debian.org/debian bookworm/main amd64 libost-conop2.3 amd64 2.3.1-9 [184 kB] Get: 207 http://deb.debian.org/debian bookworm/main amd64 libost-conop-dev amd64 2.3.1-9 [18.1 kB] Get: 208 http://deb.debian.org/debian bookworm/main amd64 libost-db2.3 amd64 2.3.1-9 [44.0 kB] Get: 209 http://deb.debian.org/debian bookworm/main amd64 libost-geom-dev amd64 2.3.1-9 [25.0 kB] Get: 210 http://deb.debian.org/debian bookworm/main amd64 libost-img2.3 amd64 2.3.1-9 [143 kB] Get: 211 http://deb.debian.org/debian bookworm/main amd64 libost-img-alg2.3 amd64 2.3.1-9 [169 kB] Get: 212 http://deb.debian.org/debian bookworm/main amd64 libost-gfx2.3 amd64 2.3.1-9 [412 kB] Get: 213 http://deb.debian.org/debian bookworm/main amd64 libost-mol-alg2.3 amd64 2.3.1-9 [327 kB] Get: 214 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB] Get: 215 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB] Get: 216 http://deb.debian.org/debian bookworm/main amd64 libost-io2.3 amd64 2.3.1-9 [609 kB] Get: 217 http://deb.debian.org/debian bookworm/main amd64 libost-seq-alg2.3 amd64 2.3.1-9 [246 kB] Get: 218 http://deb.debian.org/debian bookworm/main amd64 libegl1 amd64 1.6.0-1 [33.7 kB] Get: 219 http://deb.debian.org/debian bookworm/main amd64 libqt5dbus5 amd64 5.15.8+dfsg-11 [211 kB] Get: 220 http://deb.debian.org/debian bookworm/main amd64 libqt5network5 amd64 5.15.8+dfsg-11 [674 kB] Get: 221 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 222 http://deb.debian.org/debian bookworm/main amd64 libxcb-icccm4 amd64 0.4.1-1.1 [27.4 kB] Get: 223 http://deb.debian.org/debian bookworm/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get: 224 http://deb.debian.org/debian bookworm/main amd64 libxcb-image0 amd64 0.4.0-2 [22.9 kB] Get: 225 http://deb.debian.org/debian bookworm/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get: 226 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 227 http://deb.debian.org/debian bookworm/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get: 228 http://deb.debian.org/debian bookworm/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get: 229 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get: 230 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get: 231 http://deb.debian.org/debian bookworm/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get: 232 http://deb.debian.org/debian bookworm/main amd64 xkb-data all 2.35.1-1 [764 kB] Get: 233 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon0 amd64 1.5.0-1 [106 kB] Get: 234 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon-x11-0 amd64 1.5.0-1 [15.6 kB] Get: 235 http://deb.debian.org/debian bookworm/main amd64 libqt5gui5 amd64 5.15.8+dfsg-11 [3408 kB] Get: 236 http://deb.debian.org/debian bookworm/main amd64 libqt5widgets5 amd64 5.15.8+dfsg-11 [2383 kB] Get: 237 http://deb.debian.org/debian bookworm/main amd64 libost-gui2.3 amd64 2.3.1-9 [493 kB] Get: 238 http://deb.debian.org/debian bookworm/main amd64 libost-img-dev amd64 2.3.1-9 [39.7 kB] Get: 239 http://deb.debian.org/debian bookworm/main amd64 libost-info-dev amd64 2.3.1-9 [16.9 kB] Get: 240 http://deb.debian.org/debian bookworm/main amd64 libost-io-dev amd64 2.3.1-9 [44.8 kB] Get: 241 http://deb.debian.org/debian bookworm/main amd64 libost-mol-alg-dev amd64 2.3.1-9 [27.3 kB] Get: 242 http://deb.debian.org/debian bookworm/main amd64 libost-mol-dev amd64 2.3.1-9 [53.9 kB] Get: 243 http://deb.debian.org/debian bookworm/main amd64 libost-mol-mm2.3 amd64 2.3.1-9 [268 kB] Get: 244 http://deb.debian.org/debian bookworm/main amd64 libost-mol-mm-dev amd64 2.3.1-9 [24.9 kB] Get: 245 http://deb.debian.org/debian bookworm/main amd64 libost-seq-alg-dev amd64 2.3.1-9 [174 kB] Get: 246 http://deb.debian.org/debian bookworm/main amd64 libost-seq-dev amd64 2.3.1-9 [21.0 kB] Get: 247 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get: 248 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get: 249 http://deb.debian.org/debian bookworm/main amd64 libqt5designer5 amd64 5.15.8-2 [2748 kB] Get: 250 http://deb.debian.org/debian bookworm/main amd64 libqt5sql5 amd64 5.15.8+dfsg-11 [122 kB] Get: 251 http://deb.debian.org/debian bookworm/main amd64 libqt5help5 amd64 5.15.8-2 [149 kB] Get: 252 http://deb.debian.org/debian bookworm/main amd64 libqt5printsupport5 amd64 5.15.8+dfsg-11 [202 kB] Get: 253 http://deb.debian.org/debian bookworm/main amd64 libqt5test5 amd64 5.15.8+dfsg-11 [146 kB] Get: 254 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 255 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2 [99.3 kB] Get: 256 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2 [109 kB] Get: 257 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get: 258 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get: 259 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 260 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 261 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 262 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 263 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get: 264 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get: 265 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 266 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 267 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 268 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get: 269 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get: 270 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get: 271 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 272 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 273 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get: 274 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get: 275 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get: 276 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get: 277 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get: 278 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get: 279 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get: 280 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 281 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get: 282 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get: 283 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 284 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 285 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get: 286 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get: 287 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 288 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get: 289 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get: 290 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get: 291 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 292 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get: 293 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5.sip amd64 12.11.1-1 [56.4 kB] Get: 294 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5 amd64 5.15.9+dfsg-1 [2489 kB] Get: 295 http://deb.debian.org/debian bookworm/main amd64 python3-ost amd64 2.3.1-9 [3726 kB] Get: 296 http://deb.debian.org/debian bookworm/main amd64 openstructure amd64 2.3.1-9 [84.8 MB] Fetched 301 MB in 4s (72.8 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 ... 19591 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19907 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20341 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../018-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../019-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. 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Unpacking python3-pyparsing (3.0.9-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../255-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../256-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../257-python3-contourpy_1.0.7-1+b1_amd64.deb ... Unpacking python3-contourpy (1.0.7-1+b1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../258-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../259-python3-brotli_1.0.9-2+b6_amd64.deb ... Unpacking python3-brotli (1.0.9-2+b6) ... Selecting previously unselected package python3-decorator. 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Preparing to unpack .../278-python3-fonttools_4.38.0-1+b1_amd64.deb ... Unpacking python3-fonttools (4.38.0-1+b1) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../279-python3-kiwisolver_1.4.4-1+b1_amd64.deb ... Unpacking python3-kiwisolver (1.4.4-1+b1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../280-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../281-python3-matplotlib_3.6.3-1+b1_amd64.deb ... Unpacking python3-matplotlib (3.6.3-1+b1) ... Selecting previously unselected package python3-pyqt5.sip. Preparing to unpack .../282-python3-pyqt5.sip_12.11.1-1_amd64.deb ... Unpacking python3-pyqt5.sip (12.11.1-1) ... Selecting previously unselected package python3-pyqt5. Preparing to unpack .../283-python3-pyqt5_5.15.9+dfsg-1_amd64.deb ... Unpacking python3-pyqt5 (5.15.9+dfsg-1) ... Selecting previously unselected package python3-ost. Preparing to unpack .../284-python3-ost_2.3.1-9_amd64.deb ... Unpacking python3-ost (2.3.1-9) ... Selecting previously unselected package openstructure. Preparing to unpack .../285-openstructure_2.3.1-9_amd64.deb ... Unpacking openstructure (2.3.1-9) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libboost-system1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libwayland-server0:amd64 (1.21.0-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libdouble-conversion3:amd64 (3.2.1-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libfftw3-single3:amd64 (3.3.10-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libopenmm7.7 (7.7.0+dfsg-9+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libglvnd0:amd64 (1.6.0-1) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-21) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up xkb-data (2.35.1-1) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-21) ... Setting up file (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libost-base2.3 (2.3.1-9) ... Setting up libopengl0:amd64 (1.6.0-1) ... Setting up libboost-program-options1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up libboost-test1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libboost-program-options-dev:amd64 (1.74.0.3) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libost-geom2.3 (2.3.1-9) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libboost-system1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libdbus-1-3:amd64 (1.14.6-1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libmtdev1:amd64 (1.1.6-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libtiff6:amd64 (4.5.0-6) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libmd4c0:amd64 (0.4.8-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1) ... Setting up libboost-filesystem1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libost-geom-dev (2.3.1-9) ... Setting up libboost-python1.74.0 (1.74.0+ds1-21) ... Setting up libost-base-dev (2.3.1-9) ... Setting up libboost-test1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libevdev2:amd64 (1.13.0+dfsg-1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libboost-filesystem-dev:amd64 (1.74.0.3) ... Setting up libgudev-1.0-0:amd64 (237-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libost-mol2.3 (2.3.1-9) ... Setting up libwacom-common (2.6.0-1) ... Setting up libxkbcommon0:amd64 (1.5.0-1) ... Setting up libwayland-client0:amd64 (1.21.0-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libxcb-xinput0:amd64 (1.15-1) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libwacom9:amd64 (2.6.0-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libost-mol-dev (2.3.1-9) ... Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ... Setting up libxcb-shape0:amd64 (1.15-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libxcb-render-util0:amd64 (0.3.9-1+b1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libxcb-icccm4:amd64 (0.4.1-1.1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libxcb-util1:amd64 (0.4.0-1+b1) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up libinput-bin (1.22.1-1) ... Setting up libxcb-xkb1:amd64 (1.15-1) ... Setting up libxcb-image0:amd64 (0.4.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libboost-test-dev:amd64 (1.74.0.3) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libxcb-xinerama0:amd64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libost-conop2.3 (2.3.1-9) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libxkbcommon-x11-0:amd64 (1.5.0-1) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up libqt5core5a:amd64 (5.15.8+dfsg-11) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libqt5dbus5:amd64 (5.15.8+dfsg-11) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-10) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libqt5test5:amd64 (5.15.8+dfsg-11) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libinput10:amd64 (1.22.1-1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libgbm1:amd64 (22.3.6-1+deb12u1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libqt5network5:amd64 (5.15.8+dfsg-11) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libost-conop-dev (2.3.1-9) ... Setting up libqt5sql5:amd64 (5.15.8+dfsg-11) ... Setting up libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libqt5xml5:amd64 (5.15.8+dfsg-11) ... Setting up libegl-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libost-info2.3 (2.3.1-9) ... Setting up libcups2:amd64 (2.4.2-3) ... Setting up libegl1:amd64 (1.6.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libost-seq2.3 (2.3.1-9) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libost-img2.3 (2.3.1-9) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libost-seq-alg2.3 (2.3.1-9) ... Setting up libost-img-dev (2.3.1-9) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libost-bindings2.3 (2.3.1-9) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libost-db2.3 (2.3.1-9) ... Setting up libost-info-dev (2.3.1-9) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libost-seq-alg-dev (2.3.1-9) ... Setting up libost-seq-dev (2.3.1-9) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-pyqt5.sip (12.11.1-1) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up libost-img-alg2.3 (2.3.1-9) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up libost-gfx2.3 (2.3.1-9) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up libqt5gui5:amd64 (5.15.8+dfsg-11) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up libqt5widgets5:amd64 (5.15.8+dfsg-11) ... Setting up libqt5help5:amd64 (5.15.8-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libqt5printsupport5:amd64 (5.15.8+dfsg-11) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up libost-mol-alg2.3 (2.3.1-9) ... Setting up libost-mol-alg-dev (2.3.1-9) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libqt5designer5:amd64 (5.15.8-2) ... Setting up libboost-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-python-dev (1.74.0.3) ... Setting up libost-io2.3 (2.3.1-9) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up libost-io-dev (2.3.1-9) ... Setting up libost-mol-mm2.3 (2.3.1-9) ... Setting up python3-pyqt5 (5.15.9+dfsg-1) ... Setting up python3-scipy (1.10.1-2) ... Setting up libost-gui2.3 (2.3.1-9) ... Setting up libost-mol-mm-dev (2.3.1-9) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-ost (2.3.1-9) ... Setting up openstructure (2.3.1-9) ... Building compounds library, this may take a while... 0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3094074/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3094074/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/promod3-3.2.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../promod3_3.2.1+ds-6_source.changes dpkg-buildpackage: info: source package promod3 dpkg-buildpackage: info: source version 3.2.1+ds-6 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/promod3-3.2.1+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 && 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 12.2.0 -- The C compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Found Python: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python311 -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.53") found components: unit_test_framework -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.53") found components: filesystem system -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.53") found components: iostreams -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.53") found components: program_options -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", 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 -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/promod3-3.2.1+ds' dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make 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/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake --color= make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make 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make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake --color= make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/extras /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras/CMakeFiles/bash-completion.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_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 -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/__init__.py make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+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/promod3-3.2.1+ds/cmake_support/substitute.cmake make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make -f extras/CMakeFiles/bash-completion.dir/build.make extras/CMakeFiles/bash-completion.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_closegaps.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Generating ../../stage/lib64/python3.11/site-packages/promod3/__init__.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/core/init/__init__.py.in -DOUT_FILE=/build/promod3-3.2.1+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=3.2.1 -DGIT_BRANCH= -DGIT_COMMIT_HASH= -P /build/promod3-3.2.1+ds/cmake_support/substitute.cmake [ 1%] Generating ../stage/etc/bash_completion.d/pm-completion.bash make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Built target sidechain_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/extras && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+ds/extras/pm-completion.bash.in -DOUT_FILE=/build/promod3-3.2.1+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/promod3-3.2.1+ds/cmake_support/substitute.cmake [ 1%] Built target sidechain_data_dir [ 1%] Built target loop_pymod [ 1%] Built target scoring_pymod [ 1%] Built target scoring_data_dir [ 1%] Built target loop_data_dir cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/pm3argparse.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel [ 1%] Built target subst_pm make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Built target config_header make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_pipeline.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py [ 1%] Built target init___init__.py_pymod [ 1%] Built target core_pymod [ 1%] Built target bash-completion cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-sidechains /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py [ 1%] Built target create_stage make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring_headers.dir/build.make scoring/src/CMakeFiles/promod3_scoring_headers.dir/depend make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build make -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py [ 1%] Built target actions make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+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[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Built target init_pymod make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./check_io.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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 -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py [ 1%] Built target promod3_scripts cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_positions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./disulfid.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scoring_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./amino_acid_atoms.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./frame.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./export_helper.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./backbone.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cb_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_stems.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./backbone_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./ccd.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_hash_table.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh [ 1%] Built target modelling_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./runtime_profiling.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_closer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./density_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./superpose.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./forcefield_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_cooler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./frag_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_cruncher.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./rigid_blocks.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tree.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tetrahedral_polytope.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_group.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph_minimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./idx_handler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_reconstructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./eigen_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./loop_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./mm_system_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./motif_finder.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh [ 1%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./robin_hood.h /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./stem_geom.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_connector.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh [ 1%] Built target promod3_modelling_headers cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/superpose.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/geom_base.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/superpose.cc [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/cluster.cc.o [ 1%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tree.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/geom_stems.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/geom_base.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/cluster.cc [ 4%] Building CXX object core/src/CMakeFiles/promod3_core.dir/tetrahedral_polytope.cc.o [ 5%] Building CXX object core/src/CMakeFiles/promod3_core.dir/graph_minimizer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/tree.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/geom_stems.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/graph.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/tetrahedral_polytope.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_CORE -Dpromod3_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/src/graph_minimizer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh [ 5%] Built target promod3_scoring_headers cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh [ 5%] Built target promod3_loop_headers make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 5%] Built target promod3_sidechain_headers [ 5%] Linking CXX shared library ../../stage/lib64/libpromod3_core.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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.3.2 -o ../../stage/lib64/libpromod3_core.so.3.2.1 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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_core.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2 ../../stage/lib64/libpromod3_core.so make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 5%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o [ 5%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o [ 7%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_graph_minimizer.cc.o [ 8%] Building CXX object core/pymod/CMakeFiles/_core.dir/wrap_core.cc.o [ 8%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/all_atom_env.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/backbone.cc.o [ 9%] 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_positions.cc.o [ 9%] Building CXX object core/pymod/CMakeFiles/_core.dir/export_geom.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -MF CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o.d -o CMakeFiles/promod3_loop.dir/amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/src/amino_acid_atoms.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT core/pymod/CMakeFiles/_core.dir/export_runtime_profiling.cc.o -MF CMakeFiles/_core.dir/export_runtime_profiling.cc.o.d -o CMakeFiles/_core.dir/export_runtime_profiling.cc.o -c /build/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/all_atom_env.cc [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/frag_db.cc.o [ 9%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o [ 11%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/all_atom_positions.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/backbone.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/bb_trace_param.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/frag_db.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/forcefield_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/forcefield_lookup.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/pymod/wrap_core.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/fragger.cc.o -MF CMakeFiles/promod3_loop.dir/fragger.cc.o.d -o CMakeFiles/promod3_loop.dir/fragger.cc.o -c /build/promod3-3.2.1+ds/loop/src/fragger.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_core_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/pymod/export_geom.cc [ 12%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/density_creator.cc.o -MF CMakeFiles/promod3_loop.dir/density_creator.cc.o.d -o CMakeFiles/promod3_loop.dir/density_creator.cc.o -c /build/promod3-3.2.1+ds/loop/src/density_creator.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_constructor.cc.o -c /build/promod3-3.2.1+ds/loop/src/hydrogen_constructor.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -MF CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o.d -o CMakeFiles/promod3_loop.dir/hydrogen_rule_lookup.cc.o -c /build/promod3-3.2.1+ds/loop/src/hydrogen_rule_lookup.cc [ 14%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/src/CMakeFiles/promod3_loop.dir/idx_handler.cc.o -MF CMakeFiles/promod3_loop.dir/idx_handler.cc.o.d -o CMakeFiles/promod3_loop.dir/idx_handler.cc.o -c /build/promod3-3.2.1+ds/loop/src/idx_handler.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/loop_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/loop_object_loader.cc [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/mm_system_creator.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/mm_system_creator.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/core/pymod/export_graph_minimizer.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/core/pymod/export_runtime_profiling.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/core/pymod/export_geom.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/core/pymod/wrap_core.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/psipred_prediction.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/psipred_prediction.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/structure_db.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/structure_db.cc [ 16%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/torsion_sampler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/torsion_sampler.cc [ 18%] Building CXX object loop/src/CMakeFiles/promod3_loop.dir/sidechain_atom_rule_lookup.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_LOOP -Dpromod3_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/src/sidechain_atom_constructor.cc [ 19%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/core/_core.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_core.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 19%] Built target _core In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /usr/include/ost/base.hh:24, from /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/structure_db.hh:26, from /build/promod3-3.2.1+ds/loop/src/structure_db.cc:17: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/promod3-3.2.1+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /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/promod3-3.2.1+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++/12/ios:40: 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++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/promod3-3.2.1+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void {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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/promod3-3.2.1+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {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>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /usr/include/ost/generic_property.hh:358:38, inlined from 'void {anonymous}::AssignResidueDepths(const ost::mol::EntityView&, const ost::mol::ChainView&)' at /build/promod3-3.2.1+ds/loop/src/structure_db.cc:331:25: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void {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/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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.3.2 -o ../../stage/lib64/libpromod3_loop.so.3.2.1 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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+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.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2 ../../stage/lib64/libpromod3_loop.so make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build [ 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 loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o [ 21%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_frag_db.cc.o [ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_mm_system_creator.cc.o [ 22%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_loop_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_all_atom_env.cc [ 23%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_forcefield_lookup.cc.o [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_psipred_prediction.cc.o [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_torsion_sampler.cc.o [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_structure_db.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT loop/pymod/CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -MF CMakeFiles/_loop.dir/export_all_atom_positions.cc.o.d -o CMakeFiles/_loop.dir/export_all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_positions.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_amino_acid_atoms.cc make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_forcefield_lookup.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_frag_db.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_structure_db.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_backbone.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc [ 25%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/export_fragger.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_backbone.cc [ 26%] Building CXX object loop/pymod/CMakeFiles/_loop.dir/wrap_loop.cc.o [ 26%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_score_base.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/export_fragger.cc [ 26%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/bb_dep_rotamer_lib.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/backbone_score_base.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_loop_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/bb_dep_rotamer_lib.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/wrap_loop.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_structure_db.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_torsion_sampler.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_forcefield_lookup.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 28%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/backbone_overall_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/backbone_overall_scorer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_env.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_amino_acid_atoms.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_backbone.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_psipred_prediction.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_frag_db.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_all_atom_positions.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_loop_object_loader.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_mm_system_creator.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/loop/pymod/export_fragger.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/disulfid.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/disulfid.cc [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/frame.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/frame.cc [ 29%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/particle_scoring.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/particle_scoring.cc [ 29%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/scoring_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/scoring_object_loader.cc [ 30%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_particle_scoring.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/scwrl4_particle_scoring.cc [ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/cbeta_env_listener.cc [ 32%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_particle_scoring.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/scwrl3_particle_scoring.cc [ 32%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cb_packing_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/cb_packing_score.cc [ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_particle_scoring.cc.o [ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/vina_particle_scoring.cc [ 33%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -MF CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o.d -o CMakeFiles/promod3_sidechain.dir/rotamer_cruncher.cc.o -c /build/promod3-3.2.1+ds/sidechain/src/rotamer_cruncher.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_density.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_density.cc [ 35%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_group.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_group.cc [ 36%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_id.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_id.cc [ 36%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/cbeta_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/cbeta_score.cc [ 38%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/reduced_env_listener.cc [ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_lib.cc [ 38%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_entry.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_lib_entry.cc [ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lib_reader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_lib_reader.cc [ 39%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_connector.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/sidechain_connector.cc [ 39%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/reduced_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/reduced_score.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/sidechain_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/sidechain_object_loader.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_constructor.cc [ 40%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/rotamer_lookup.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/rotamer_lookup.cc [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/clash_env_listener.cc [ 42%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/clash_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/clash_score.cc [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl4_rotamer_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/scwrl4_rotamer_constructor.cc [ 43%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/scwrl3_rotamer_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/scwrl3_rotamer_constructor.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/vina_rotamer_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/vina_rotamer_constructor.cc [ 45%] Building CXX object sidechain/src/CMakeFiles/promod3_sidechain.dir/subrotamer_optimizer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SIDECHAIN -Dpromod3_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/src/subrotamer_optimizer.cc [ 45%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/loop/_loop.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_loop.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 [ 45%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/density_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/density_score.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/hbond_env_listener.cc [ 46%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/hbond_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/hbond_score.cc make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 46%] Built target _loop [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/ss_agreement_score.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/ss_agreement_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/ss_agreement_env_listener.cc [ 47%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/torsion_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/torsion_score.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/pairwise_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/pairwise_score.cc [ 49%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/constraint_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/constraint_constructor.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_overall_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/all_atom_overall_scorer.cc [ 50%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/all_atom_interaction_env_listener.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_interaction_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/all_atom_interaction_score.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_packing_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/all_atom_packing_score.cc [ 52%] Building CXX object scoring/src/CMakeFiles/promod3_scoring.dir/all_atom_clash_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_SCORING -Dpromod3_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/src/all_atom_clash_score.cc [ 53%] Linking CXX shared library ../../stage/lib64/libpromod3_scoring.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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.3.2 -o ../../stage/lib64/libpromod3_scoring.so.3.2.1 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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+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.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_scoring.so.3.2 ../../stage/lib64/libpromod3_scoring.so make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 53%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 53%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_backbone_score.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_backbone_score.cc [ 53%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_constraint_constructor.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_pairwise_functions.cc.o [ 54%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_object_loader.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_all_atom_score.cc.o [ 56%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/wrap_scoring.cc.o [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_scwrl3_energy_functions.cc.o [ 57%] Building CXX object scoring/pymod/CMakeFiles/_scoring.dir/export_density_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_object_loader.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_pairwise_functions.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_scwrl3_energy_functions.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/export_density_scorer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_scoring_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/pymod/wrap_scoring.cc [ 59%] Linking CXX shared library ../../stage/lib64/libpromod3_sidechain.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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.3.2 -o ../../stage/lib64/libpromod3_sidechain.so.3.2.1 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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+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.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2 ../../stage/lib64/libpromod3_sidechain.so make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 59%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 59%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o [ 59%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_connector.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_disulfid.cc.o -MF CMakeFiles/_sidechain.dir/export_disulfid.cc.o.d -o CMakeFiles/_sidechain.dir/export_disulfid.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_disulfid.cc [ 60%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_connector.cc [ 61%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -MF CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o.d -o CMakeFiles/promod3_modelling.dir/extension_scheme.cc.o -c /build/promod3-3.2.1+ds/modelling/src/extension_scheme.cc [ 61%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_frame.cc.o -MF CMakeFiles/_sidechain.dir/export_frame.cc.o.d -o CMakeFiles/_sidechain.dir/export_frame.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_frame.cc [ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap.cc.o -MF CMakeFiles/promod3_modelling.dir/gap.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap.cc.o -c /build/promod3-3.2.1+ds/modelling/src/gap.cc [ 63%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_graph.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_graph.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_particle.cc.o -MF CMakeFiles/_sidechain.dir/export_particle.cc.o.d -o CMakeFiles/_sidechain.dir/export_particle.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -MF CMakeFiles/promod3_modelling.dir/gap_extender.cc.o.d -o CMakeFiles/promod3_modelling.dir/gap_extender.cc.o -c /build/promod3-3.2.1+ds/modelling/src/gap_extender.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_density_scorer.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_pairwise_functions.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/wrap_scoring.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_scwrl3_energy_functions.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_all_atom_score.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_object_loader.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_backbone_score.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/scoring/pymod/export_constraint_constructor.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer.cc [ 64%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/model.cc.o -MF CMakeFiles/promod3_modelling.dir/model.cc.o.d -o CMakeFiles/promod3_modelling.dir/model.cc.o -c /build/promod3-3.2.1+ds/modelling/src/model.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_frame.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_connector.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_disulfid.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_graph.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_cruncher.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_particle.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/all_atom_relaxer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/all_atom_relaxer.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/src/CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -MF CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o.d -o CMakeFiles/promod3_modelling.dir/backbone_relaxer.cc.o -c /build/promod3-3.2.1+ds/modelling/src/backbone_relaxer.cc [ 67%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/ccd.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/ccd.cc [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -MF CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o.d -o CMakeFiles/_sidechain.dir/export_rotamer_density.cc.o -c /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_density.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_ids.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_ids.cc [ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_lib.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc [ 69%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_sidechain_object_loader.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_cruncher.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/kic.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/kic.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_rotamer_constructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_density.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/export_subrotamer_optimizer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/export_subrotamer_optimizer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_ids.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_sidechain_object_loader.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_lib.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/loop_candidate.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/loop_candidate.cc [ 71%] Building CXX object sidechain/pymod/CMakeFiles/_sidechain.dir/wrap_sidechain.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_sidechain_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/pymod/wrap_sidechain.cc [ 71%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/monte_carlo.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_closer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/monte_carlo_closer.cc [ 73%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_cooler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/monte_carlo_cooler.cc [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_sampler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/monte_carlo_sampler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_rotamer_constructor.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/monte_carlo_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/monte_carlo_scorer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/export_subrotamer_optimizer.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/rigid_blocks.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/rigid_blocks.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/sidechain/pymod/wrap_sidechain.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/score_container.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/score_container.cc [ 76%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/scoring_weights.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/scoring_weights.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_reconstructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/sidechain_reconstructor.cc [ 77%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/sidechain_env_listener.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/sidechain_env_listener.cc [ 78%] Building CXX object modelling/src/CMakeFiles/promod3_modelling.dir/motif_finder.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DPROMOD3_MODULE_PROMOD3_MODELLING -Dpromod3_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/src/motif_finder.cc [ 80%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/scoring/_scoring.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_scoring.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 80%] Built target _scoring In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/Dense:1, from /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/eigen_types.hh:23, from /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/superpose.hh:24, from /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/backbone.hh:33, from /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/kic.hh:21, from /build/promod3-3.2.1+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/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_sidechain.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 81%] Built target _sidechain [ 81%] Linking CXX shared library ../../stage/lib64/libpromod3_modelling.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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.3.2 -o ../../stage/lib64/libpromod3_modelling.so.3.2.1 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 -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+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.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E cmake_symlink_library ../../stage/lib64/libpromod3_modelling.so.3.2.1 ../../stage/lib64/libpromod3_modelling.so.3.2 ../../stage/lib64/libpromod3_modelling.so make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 81%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o [ 83%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_extension_scheme.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_closure.cc.o -MF CMakeFiles/_modelling.dir/export_loop_closure.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_closure.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc [ 84%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o [ 85%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o [ 87%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o [ 88%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/wrap_modelling.cc.o [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o [ 90%] Building CXX object modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/pymod/export_extension_scheme.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap.cc.o -MF CMakeFiles/_modelling.dir/export_gap.cc.o.d -o CMakeFiles/_modelling.dir/export_gap.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_gap.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_gap_extender.cc.o -MF CMakeFiles/_modelling.dir/export_gap_extender.cc.o.d -o CMakeFiles/_modelling.dir/export_gap_extender.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_gap_extender.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -MF CMakeFiles/_modelling.dir/export_loop_candidate.cc.o.d -o CMakeFiles/_modelling.dir/export_loop_candidate.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_loop_candidate.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_model.cc.o -MF CMakeFiles/_modelling.dir/export_model.cc.o.d -o CMakeFiles/_modelling.dir/export_model.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_model.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -MF CMakeFiles/_modelling.dir/export_monte_carlo.cc.o.d -o CMakeFiles/_modelling.dir/export_monte_carlo.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_monte_carlo.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -MF CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o.d -o CMakeFiles/_modelling.dir/export_rigid_blocks.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_rigid_blocks.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_score_container.cc.o -MF CMakeFiles/_modelling.dir/export_score_container.cc.o.d -o CMakeFiles/_modelling.dir/export_score_container.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_score_container.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -MF CMakeFiles/_modelling.dir/export_scoring_weights.cc.o.d -o CMakeFiles/_modelling.dir/export_scoring_weights.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_scoring_weights.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -MF CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o.d -o CMakeFiles/_modelling.dir/export_sidechain_reconstructor.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_sidechain_reconstructor.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modelling/pymod/CMakeFiles/_modelling.dir/export_motif_finder.cc.o -MF CMakeFiles/_modelling.dir/export_motif_finder.cc.o.d -o CMakeFiles/_modelling.dir/export_motif_finder.cc.o -c /build/promod3-3.2.1+ds/modelling/pymod/export_motif_finder.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -D_modelling_EXPORTS -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/pymod/wrap_modelling.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_motif_finder.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_extension_scheme.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_scoring_weights.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/wrap_modelling.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_score_container.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_gap_extender.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_gap.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_rigid_blocks.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_sidechain_reconstructor.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_model.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_loop_closure.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_monte_carlo.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/promod3-3.2.1+ds/modelling/pymod/export_loop_candidate.cc:17: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 90%] Linking CXX shared module ../../stage/lib64/python3.11/site-packages/promod3/modelling/_modelling.so cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/wrap_modelling.cc.o -L/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64: ../../stage/lib64/libpromod3_modelling.so.3.2.1 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so.1.74.0 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[3]: Leaving directory '/build/promod3-3.2.1+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 -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data 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'/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake --color= make -f 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'/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+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 loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build make[3]: Entering directory '/build/promod3-3.2.1+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]: Entering directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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 [ 90%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_helical.dat [ 91%] Generating ../../stage/share/promod3/loop_data/torsion_sampler.dat [ 91%] Generating ../../stage/share/promod3/loop_data/structure_db.dat [ 92%] Generating ../../stage/share/promod3/loop_data/ff_lookup_charmm.dat [ 92%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_coil.dat [ 92%] Generating ../../stage/share/promod3/loop_data/frag_db.dat [ 94%] Generating ../../stage/share/promod3/loop_data/torsion_sampler_extended.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/cbeta_scorer.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/aa_packing_scorer.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/cb_packing_scorer.dat [ 95%] Generating ../../stage/share/promod3/scoring_data/reduced_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_helical.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_helical.dat'\ TorsionSampler cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_structure_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/structure_db.dat'\ StructureDB cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler.dat'\ TorsionSampler cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_ff_lookup_charmm.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/ff_lookup_charmm.dat'\ ForcefieldLookup cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cb_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cb_packing_scorer.dat'\ CBPackingScorer cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_extended.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_extended.dat'\ TorsionSampler cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_aa_packing_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_packing_scorer.dat'\ AllAtomPackingScorer cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_cbeta_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/cbeta_scorer.dat'\ CBetaScorer cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_frag_db.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/frag_db.dat'\ FragDB [ 95%] Generating ../../stage/share/promod3/scoring_data/hbond_scorer.dat make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_reduced_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/reduced_scorer.dat'\ ReducedScorer cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_hbond_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/hbond_scorer.dat'\ HBondScorer [ 95%] Generating ../../stage/share/promod3/scoring_data/torsion_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/loop/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/loop/data/portable_torsion_sampler_coil.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data/torsion_sampler_coil.dat'\ TorsionSampler [ 97%] Generating ../../stage/share/promod3/scoring_data/ss_agreement_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_torsion_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/torsion_scorer.dat'\ TorsionScorer cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_ss_agreement_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/ss_agreement_scorer.dat'\ SSAgreementScorer [ 98%] Generating ../../stage/share/promod3/scoring_data/aa_scorer.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/scoring/data/convert_binaries.py'\ '/build/promod3-3.2.1+ds/scoring/data/portable_aa_scorer.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data/aa_scorer.dat'\ AllAtomInteractionScorer make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] Built target generate_scoring_data_torsion_scorer.dat make -f sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/depend make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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 [ 98%] Built target generate_scoring_data_aa_packing_scorer.dat make[3]: Entering directory '/build/promod3-3.2.1+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/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake --color= [ 98%] Built target generate_scoring_data_aa_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] Built target generate_scoring_data_cb_packing_scorer.dat [ 98%] Built target generate_scoring_data_ss_agreement_scorer.dat [100%] Generating ../../stage/share/promod3/sidechain_data/bb_dep_lib.dat [100%] Built target generate_loop_data_ff_lookup_charmm.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_bb_dep_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/bb_dep_lib.dat'\ BBDepRotamerLib [100%] Built target generate_scoring_data_hbond_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Generating ../../stage/share/promod3/sidechain_data/lib.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && sh -c PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/\ /usr/bin/python3\ '/build/promod3-3.2.1+ds/sidechain/data/convert_lib.py'\ '/build/promod3-3.2.1+ds/sidechain/data/portable_lib.dat'\ '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data/lib.dat'\ RotamerLib make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_reduced_scorer.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_scoring_data_cbeta_scorer.dat make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/depend make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target scoring_data make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+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 make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_torsion_sampler_helical.dat [100%] Built target generate_loop_data_torsion_sampler_coil.dat make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_sidechain_data_lib.dat make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target sidechain_data make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target generate_loop_data_frag_db.dat make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target loop_data make[2]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j15 check ARGS\+=--verbose ARGS\+=-j15 make[1]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[2]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles 93 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make -f core/tests/CMakeFiles/test_data_core.dir/build.make core/tests/CMakeFiles/test_data_core.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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_data_core.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/CMakeFiles/config_header.dir/DependInfo.cmake --color= make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/depend make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/core_pymod.dir/DependInfo.cmake --color= make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_pymod.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data_dir.dir/DependInfo.cmake --color= make -f core/init/CMakeFiles/init___init__.py_pymod.dir/build.make core/init/CMakeFiles/init___init__.py_pymod.dir/depend make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/modelling_pymod.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/loop_pymod.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/scoring_pymod.dir/DependInfo.cmake --color= make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/sidechain_pymod.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init___init__.py_pymod.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data_dir.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data_dir.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_data_modelling.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/subst_pm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make -f config/src/CMakeFiles/config_header.dir/build.make config/src/CMakeFiles/config_header.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-model /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-model make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/config/src/config.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/config.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/core_pymod.dir/build.make core/pymod/CMakeFiles/core_pymod.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/loop_pymod.dir/build.make loop/pymod/CMakeFiles/loop_pymod.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 -f loop/data/CMakeFiles/loop_data_dir.dir/build.make loop/data/CMakeFiles/loop_data_dir.dir/build make -f scoring/pymod/CMakeFiles/scoring_pymod.dir/build.make scoring/pymod/CMakeFiles/scoring_pymod.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/__init__.py make -f scoring/data/CMakeFiles/scoring_data_dir.dir/build.make scoring/data/CMakeFiles/scoring_data_dir.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/loop/__init__.py make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/loop_data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/scoring/__init__.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/scoring_data make -f modelling/pymod/CMakeFiles/modelling_pymod.dir/build.make modelling/pymod/CMakeFiles/modelling_pymod.dir/build make -f sidechain/pymod/CMakeFiles/sidechain_pymod.dir/build.make sidechain/pymod/CMakeFiles/sidechain_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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/src/CMakeFiles/create_stage.dir/build.make core/src/CMakeFiles/create_stage.dir/build make -f sidechain/data/CMakeFiles/sidechain_data_dir.dir/build.make sidechain/data/CMakeFiles/sidechain_data_dir.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/__init__.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/pymod/__init__.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/sidechain/__init__.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/init/CMakeFiles/init___init__.py_pymod.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/share/promod3/sidechain_data make -f modelling/tests/CMakeFiles/test_data_modelling.dir/build.make modelling/tests/CMakeFiles/test_data_modelling.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/subst_pm.dir/build.make scripts/CMakeFiles/subst_pm.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-rawmodel /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-rawmodel make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/promod3-3.2.1+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/promod3-3.2.1+ds/cmake_support/substitute.cmake make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests//test_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core//test_helper.py make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_closegaps.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_closegaps.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/helper.py make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 1%] Built target init___init__.py_pymod make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/depend [ 1%] Built target config_header [ 1%] Built target loop_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_molprobity.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_molprobity.py make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/init_pymod.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-help /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-help cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/pymod/pm3argparse.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/core/pm3argparse.py [ 1%] Built target loop_data_dir [ 1%] Built target sidechain_pymod [ 1%] Built target scoring_data_dir [ 1%] Built target scoring_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.fasta [ 1%] Built target sidechain_data_dir [ 1%] Built target subst_pm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_pipeline.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_pipeline.py make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/CMakeFiles/promod3_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/init/CMakeFiles/init_pymod.dir/build.make core/init/CMakeFiles/init_pymod.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/pm-build-sidechains /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/libexec/promod3/pm-build-sidechains make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/broken_on_purpose.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/broken_on_purpose.chemlib make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/init/CMakeFiles/init_pymod.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_ring_punches.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_ring_punches.py [ 1%] Built target core_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1cjx-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1cjx-1.pdb.gz cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl [ 1%] Built target init_pymod make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scripts/CMakeFiles/promod3_scripts.dir/build.make scripts/CMakeFiles/promod3_scripts.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_denovo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_denovo.py [ 1%] Built target actions cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.fasta [ 1%] Built target create_stage cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make -f actions/tests/CMakeFiles/test_data_actions.dir/build.make actions/tests/CMakeFiles/test_data_actions.dir/depend make -f core/src/CMakeFiles/promod3_core_headers.dir/build.make core/src/CMakeFiles/promod3_core_headers.dir/depend make -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_data_actions.dir/DependInfo.cmake --color= 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 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scripts/pm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/bin/pm make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core_headers.dir/DependInfo.cmake --color= make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling_headers.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_fragger_handle.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_fragger_handle.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 -f loop/src/CMakeFiles/promod3_loop_headers.dir/build.make loop/src/CMakeFiles/promod3_loop_headers.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./check_io.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./check_io.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_env.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_env.hh make[4]: Leaving directory '/build/promod3-3.2.1+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 -f sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain_headers.dir/build make -f modelling/src/CMakeFiles/promod3_modelling_headers.dir/build.make modelling/src/CMakeFiles/promod3_modelling_headers.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./bb_dep_rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./bb_dep_rotamer_lib.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_score_base.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./extension_scheme.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./extension_scheme.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_reconstruct_sidechains.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_reconstruct_sidechains.py [ 1%] Built target promod3_scripts cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./cluster.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./cluster.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./all_atom_positions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./all_atom_positions.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./backbone_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./backbone_overall_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./disulfid.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./disulfid.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRN.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_monte_carlo.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_monte_carlo.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/gly.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/gly.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./dynamic_spatial_organizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./dynamic_spatial_organizer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./gap_extender.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./gap_extender.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./amino_acid_atoms.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./amino_acid_atoms.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scoring_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scoring_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./frame.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./frame.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_mhandle_helper.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_mhandle_helper.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./model.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./model.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./export_helper.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./export_helper.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./backbone.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./backbone.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_graph.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/seq.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/seq.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_build.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_build.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_alignment_fiddling.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_alignment_fiddling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./all_atom_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./all_atom_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./bb_trace_param.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./bb_trace_param.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cb_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cb_packing_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./backbone_relaxer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./backbone_relaxer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/pymod/_raw_model.py /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages//promod3/modelling/_raw_model.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./data_bag.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./data_bag.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_A.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./geom_stems.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./geom_stems.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./cbeta_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./cbeta_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/actions/tests/data/seq_ins.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions/data/seq_ins.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./ccd.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./ccd.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_hash_table.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_hash_table.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./message.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./message.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_env_listener.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./kic.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./kic.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh [ 1%] Built target modelling_pymod cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_sink.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_sink.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./reduced_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./reduced_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2aoh-1_cut_B.fasta [ 1%] 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 -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 -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 -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_actions.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-model.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_build-rawmodel.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/actions/tests/CMakeFiles/test_action_help.py_run.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_final.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_final.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./loop_candidate.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./loop_candidate.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./dense_map.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./dense_map.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_data_source.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_data_source.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 -f actions/tests/CMakeFiles/test_actions.py_run.dir/build.make actions/tests/CMakeFiles/test_actions.py_run.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make -f actions/tests/CMakeFiles/test_action_help.py_run.dir/build.make actions/tests/CMakeFiles/test_action_help.py_run.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./density_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./density_creator.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./clash_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./portable_binary_serializer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./portable_binary_serializer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_particle_scoring.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_particle_scoring.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.aln /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.aln [ 2%] running checks test_action_build-rawmodel.py [ 2%] running checks test_action_build-model.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_build-rawmodel.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_build-model.py" [ 2%] running checks test_actions.py [ 3%] running checks test_action_help.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_rec.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./forcefield_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./forcefield_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_closer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_closer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_action_help.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/actions && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/actions/tests/test_actions.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./density_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./density_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./runtime_profiling.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./runtime_profiling.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./frag_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./frag_db.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_cooler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_cooler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./superpose.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./superpose.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_cruncher.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_cruncher.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./fragger.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./fragger.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_sampler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./enumerator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./enumerator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./hbond_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./hbond_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_density.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_density.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./monte_carlo_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./monte_carlo_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_group.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_group.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.json /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.json cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./hydrogen_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./hydrogen_rule_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./rigid_blocks.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./rigid_blocks.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1crn_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1crn_sc_test.pdb . ---------------------------------------------------------------------- Ran 1 test in 0.000s OK cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tree.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tree.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./ss_agreement_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./ss_agreement_env_listener.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_id.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_id.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./idx_handler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./idx_handler.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./score_container.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./score_container.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./tetrahedral_polytope.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./tetrahedral_polytope.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./torsion_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./torsion_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/2jlp-1.pdb [ 3%] Built target test_actions.py_run cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./loop_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./loop_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./graph_minimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./graph_minimizer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./scoring_weights.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./scoring_weights.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1CRNA.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1CRNA.hhm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_scoring_function.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_scoring_function.hh .. ---------------------------------------------------------------------- Ran 2 tests in 0.059s OK cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_entry.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_entry.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./mm_system_creator.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./mm_system_creator.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_reconstructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_reconstructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/src/./eigen_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/core/./eigen_types.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./pairwise_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./pairwise_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lib_reader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lib_reader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./psipred_prediction.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./psipred_prediction.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./sidechain_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./sidechain_env_listener.hh [ 3%] Built target test_action_help.py_run cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye.pdb make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_connector.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_connector.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./constraint_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./constraint_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./stem_geom.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./stem_geom.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./motif_finder.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./motif_finder.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl [ 3%] Built target promod3_core_headers make -f core/src/CMakeFiles/promod3_core.dir/build.make core/src/CMakeFiles/promod3_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/src/CMakeFiles/promod3_core.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./sidechain_object_loader.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./sidechain_object_loader.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_score_base.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_score_base.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/src/./robin_hood.h /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/modelling/./robin_hood.h cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_A.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_rec.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_rec.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_overall_scorer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_overall_scorer.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./torsion_sampler.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./torsion_sampler.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./rotamer_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./rotamer_lookup.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_env_listener.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_env_listener.hh [ 3%] Built target promod3_modelling_headers cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./ushort_vec.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./ushort_vec.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5d52-1_cut_B.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl4_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_interaction_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_interaction_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1eye_sc_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1eye_sc_test.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_rule_lookup.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_rule_lookup.hh make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/src/CMakeFiles/promod3_core.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./scwrl3_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_packing_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_packing_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./sidechain_atom_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./sidechain_atom_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 6%] Built target promod3_core make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/pymod/CMakeFiles/_core.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./vina_rotamer_constructor.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./vina_rotamer_constructor.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn.hhm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/src/./structure_db_custom_types.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/loop/./structure_db_custom_types.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./all_atom_clash_score.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./all_atom_clash_score.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1ITX-A-11_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1ITX-A-11_sidechain.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/src/./subrotamer_optimizer.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/sidechain/./subrotamer_optimizer.hh make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/src/./scwrl3_energy_functions.hh /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include/promod3/scoring/./scwrl3_energy_functions.hh cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f core/pymod/CMakeFiles/_core.dir/build.make core/pymod/CMakeFiles/_core.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/1crn_corrupted.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/1crn_corrupted.hhm [ 6%] Built target promod3_loop_headers cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1K5C-A-16_clash.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1K5C-A-16_clash.pdb make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/depend make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 6%] Built target promod3_sidechain_headers make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/src/CMakeFiles/promod3_loop.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl [ 6%] Built target promod3_scoring_headers make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/pymod/CMakeFiles/_core.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.fasta [ 8%] Built target _core cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/1mcg.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/1mcg.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/aln_tpl/5ua4_B.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/aln_tpl/5ua4_B.hhm cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/alignment.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/alignment.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/src/CMakeFiles/promod3_loop.dir/build.make loop/src/CMakeFiles/promod3_loop.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_A.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/src/CMakeFiles/promod3_loop.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2aoh-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2aoh-1_cut_B.fasta [ 17%] 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 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_1.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_1.fas make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/pymod/CMakeFiles/_loop.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/src/CMakeFiles/promod3_scoring.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/src/CMakeFiles/promod3_sidechain.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2dbs.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2dbs.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_2trg.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_2trg.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_3.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_3.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake.fas.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake.fas.gz cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2jlp-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2jlp-1.pdb make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/pymod/CMakeFiles/_loop.dir/build.make loop/pymod/CMakeFiles/_loop.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_nel.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_nel.fas make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/src/CMakeFiles/promod3_sidechain.dir/build.make sidechain/src/CMakeFiles/promod3_sidechain.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/src/CMakeFiles/promod3_scoring.dir/build.make scoring/src/CMakeFiles/promod3_scoring.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/pymod/CMakeFiles/_loop.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/core/tests/data/fasta/1ake_sw.fas /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/data/fasta/1ake_sw.fas cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/2xim-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/2xim-1.pdb.gz [ 22%] Built target _loop make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/src/CMakeFiles/promod3_sidechain.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 33%] Built target promod3_sidechain make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/depend [ 33%] Built target test_data_core make -f core/tests/CMakeFiles/test_suite_core.dir/build.make core/tests/CMakeFiles/test_suite_core.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/pymod/CMakeFiles/_sidechain.dir/DependInfo.cmake --color= make -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/depend make -f core/tests/CMakeFiles/test_helper.py_run.dir/build.make core/tests/CMakeFiles/test_helper.py_run.dir/depend make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_helper.py_run.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_pm3argparse.py_run.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.pdb.gz make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/src/CMakeFiles/promod3_scoring.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 -f core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build.make core/tests/CMakeFiles/test_setcompoundschemlib.py_run.dir/build make -f core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build.make core/tests/CMakeFiles/test_pm3argparse.py_run.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 44%] Built target promod3_scoring make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/pymod/CMakeFiles/_scoring.dir/DependInfo.cmake --color= make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/depend [ 45%] running checks test_helper.py [ 45%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_check_io.cc.o [ 46%] running checks test_setcompoundschemlib.py [ 47%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_portable_binary.cc.o [ 47%] running checks test_pm3argparse.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/tests/test_check_io.cc [ 48%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/test_graph_minimizer.cc.o [ 48%] Building CXX object core/tests/CMakeFiles/test_suite_core.dir/tests.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_helper.py" make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/src/CMakeFiles/promod3_modelling.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_setcompoundschemlib.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/tests/test_portable_binary.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/tests/test_graph_minimizer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/core/tests/test_pm3argparse.py" cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/core/tests/tests.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/3b08-3.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/3b08-3.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4nyk.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/pymod/CMakeFiles/_scoring.dir/build.make scoring/pymod/CMakeFiles/_scoring.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/pymod/CMakeFiles/_sidechain.dir/build.make sidechain/pymod/CMakeFiles/_sidechain.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4R6K-A-13_sidechain.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4R6K-A-13_sidechain.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/pymod/CMakeFiles/_scoring.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/src/CMakeFiles/promod3_modelling.dir/build.make modelling/src/CMakeFiles/promod3_modelling.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.pdb.gz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.pdb.gz make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/pymod/CMakeFiles/_sidechain.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 52%] Built target _scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 59%] Built target _sidechain cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/4ksl-1.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/4ksl-1.fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modelling/src/CMakeFiles/promod3_modelling.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 68%] Built target promod3_modelling make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/pymod/CMakeFiles/_modelling.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut.pdb ..........cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data ......................cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_A.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_A.fasta ........ .---------------------------------------------------------------------- Ran 2 tests in 0.090s OK .......... ---------------------------------------------------------------------- Ran 12 tests in 0.004s OK ....cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/5d52-1_cut_B.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/5d52-1_cut_B.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f modelling/pymod/CMakeFiles/_modelling.dir/build.make modelling/pymod/CMakeFiles/_modelling.dir/build make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 68%] Built target test_setcompoundschemlib.py_run cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.fasta [ 68%] Built target test_helper.py_run cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'modelling/pymod/CMakeFiles/_modelling.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/CA-3cm91E.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/CA-3cm91E.pdb .[ 75%] Built target _modelling make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/init/CMakeFiles/_init.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' .make -f core/init/CMakeFiles/_init.dir/build.make core/init/CMakeFiles/_init.dir/build .make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'core/init/CMakeFiles/_init.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.fasta [ 75%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/DependInfo.cmake --color= make -f loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build make -f 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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build make -f loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build.make loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build make -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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_ff_lookup_charmm.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_coil.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_extended.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_torsion_sampler_helical.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_frag_db.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 76%] Built target generate_loop_data_torsion_sampler.dat [ 76%] Built target generate_loop_data_torsion_sampler_coil.dat [ 77%] Built target generate_loop_data_ff_lookup_charmm.dat [ 78%] Built target generate_loop_data_torsion_sampler_extended.dat 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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/DependInfo.cmake --color= [ 78%] Built target generate_loop_data_torsion_sampler_helical.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/build 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 -f scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/depend make -f scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/generate_loop_data_structure_db.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/DependInfo.cmake --color= make -f scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build.make scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/cbeta.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/cbeta.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/DependInfo.cmake --color= [ 78%] Built target generate_loop_data_frag_db.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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/DependInfo.cmake --color= [ 78%] Built target generate_loop_data_structure_db.dat make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cb_packing_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_cbeta_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_reduced_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data 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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_packing_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/generate_scoring_data_torsion_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/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_hbond_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_ss_agreement_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 78%] Built target generate_scoring_data_cb_packing_scorer.dat [ 79%] Built target generate_scoring_data_cbeta_scorer.dat [ 79%] Built target generate_scoring_data_reduced_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 -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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+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_lib.dat.dir/build.make sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/compounds.chemlib /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/compounds.chemlib make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/DependInfo.cmake --color= 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_torsion_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 80%] Built target generate_scoring_data_hbond_scorer.dat [ 80%] Built target generate_scoring_data_ss_agreement_scorer.dat make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/depend [ 80%] Built target generate_scoring_data_aa_packing_scorer.dat make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/data/CMakeFiles/loop_data.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/generate_scoring_data_aa_scorer.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_lib.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 80%] Built target generate_scoring_data_torsion_scorer.dat make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/generate_sidechain_data_bb_dep_lib.dat.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/data/CMakeFiles/loop_data.dir/build.make loop/data/CMakeFiles/loop_data.dir/build [ 80%] Built target generate_sidechain_data_lib.dat make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'loop/data/CMakeFiles/loop_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 81%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/data/CMakeFiles/scoring_data.dir/DependInfo.cmake --color= [ 82%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/data/CMakeFiles/sidechain_data.dir/DependInfo.cmake --color= [ 82%] Built target loop_data make -f loop/tests/CMakeFiles/test_data_loop.dir/build.make loop/tests/CMakeFiles/test_data_loop.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_data_loop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f sidechain/data/CMakeFiles/sidechain_data.dir/build.make sidechain/data/CMakeFiles/sidechain_data.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'sidechain/data/CMakeFiles/sidechain_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f scoring/data/CMakeFiles/scoring_data.dir/build.make scoring/data/CMakeFiles/scoring_data.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'scoring/data/CMakeFiles/scoring_data.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 82%] Built target scoring_data make -f scoring/tests/CMakeFiles/test_data_scoring.dir/build.make scoring/tests/CMakeFiles/test_data_scoring.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data [ 82%] Built target sidechain_data make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_data_scoring.dir/DependInfo.cmake --color= make -f sidechain/tests/CMakeFiles/test_data_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_data_sidechain.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_data_sidechain.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A.hhm /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.hhm make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain .make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/del.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/del.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/1CRNA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/1CRNA.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/sidechain/tests/data/all_sc.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/data/all_sc.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1A88A_with_gap.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1A88A_with_gap.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ff_NAD.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ff_NAD.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/3DEFA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/3DEFA.pdb [ 82%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1akyA.horiz /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1akyA.horiz make -f sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build.make sidechain/tests/CMakeFiles/test_suite_sidechain.dir/build cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/scoring/tests/data/clash_test.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/data/clash_test.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data [ 82%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/tests.cc.o [ 82%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o [ 83%] Building CXX object sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_rotamers.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT sidechain/tests/CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -MF CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o.d -o CMakeFiles/test_suite_sidechain.dir/test_frame_construction.cc.o -c /build/promod3-3.2.1+ds/sidechain/tests/test_frame_construction.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/tests/test_rotamers.cc make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/sidechain/tests/tests.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_on_top.pdb [ 83%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring.dir/DependInfo.cmake --color= cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/1CRN.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/1CRN.pdb .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data make[4]: Leaving directory '/build/promod3-3.2.1+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 cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/3DEFA.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/3DEFA.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_almost_on_top.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_almost_on_top.pdb make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_score_base.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/tests/test_backbone_score_base.cc [ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_backbone_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/tests/test_backbone_scorer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 84%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/test_all_atom_scorer.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/tests/test_all_atom_scorer.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/4nyk.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/4nyk.pdb ..cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/gly_shifted_nter.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/gly_shifted_nter.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/hetero-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/hetero-punched.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data .. ---------------------------------------------------------------------- Ran 3 tests in 1.873s OK cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hisd.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hisd.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ins.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ins.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/modelCApartial-5tgl1A.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/modelCApartial-5tgl1A.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hise.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hise.pdb [ 84%] Built target test_action_build-rawmodel.py_run [ 86%] Building CXX object scoring/tests/CMakeFiles/test_suite_scoring.dir/tests.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/scoring/tests/tests.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/neighbor-punched.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/neighbor-punched.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_polar_hish.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_polar_hish.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_frag_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_frag_db.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/all_aa_prot_ref.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/all_aa_prot_ref.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/loop/tests/data/CHARMM27.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/data/CHARMM27.dat cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/port_str_db.dat /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/port_str_db.dat make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 86%] Built target test_data_loop make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/depend cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/sep.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.fasta make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f loop/tests/CMakeFiles/test_suite_loop.dir/build.make loop/tests/CMakeFiles/test_suite_loop.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data [ 86%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_env.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_env.cc cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/sep.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/sep.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/seq.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/seq.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/smtl2bl4.1.pdb /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/smtl2bl4.1.pdb cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/ter.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/ter.fasta .cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/terminal_deletion_aln.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/terminal_deletion_aln.fasta cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E make_directory /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/cmake -E copy_if_different /build/promod3-3.2.1+ds/modelling/tests/data/double_gap_aln.fasta /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/data/double_gap_aln.fasta make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 86%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 87%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_candidates.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/tests/test_loop_candidates.cc [ 87%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_loop_closing.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/tests/test_loop_closing.cc ............ ---------------------------------------------------------------------- Ran 66 tests in 3.050s OK make[4]: Leaving directory '/build/promod3-3.2.1+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/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_close_gaps.py_run.dir/DependInfo.cmake --color= [ 87%] Built target test_pm3argparse.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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_gap_extension.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/promod3-3.2.1+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 [ 88%] running checks test_gap_extension.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_gap_extension.py" make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 88%] running checks test_close_gaps.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_close_gaps.py" [ 89%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/test_sidechain_reconstructor.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/tests/test_sidechain_reconstructor.cc ...... ---------------------------------------------------------------------- Ran 6 tests in 0.050s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_modelling.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] running checks test_modelling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_modelling.py" ......................... ---------------------------------------------------------------------- Ran 25 tests in 0.356s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_pipeline.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] running checks test_pipeline.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_pipeline.py" .make -f modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/build.make modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_ring_punches.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] running checks test_ring_punches.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_ring_punches.py" ... ---------------------------------------------------------------------- Ran 2 tests in 0.338s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 89%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_sidechain_reconstruction.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 90%] running checks test_sidechain_reconstruction.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_sidechain_reconstruction.py" ... ---------------------------------------------------------------------- Ran 3 tests in 9.492s OK [ 90%] Building CXX object modelling/tests/CMakeFiles/test_suite_modelling.dir/tests.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/modelling/tests/tests.cc make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 90%] Built target test_action_build-model.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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_alignment_fiddling.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 90%] running checks test_alignment_fiddling.py cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && sh -c "PYTHONPATH=/usr/lib/python3/dist-packages:/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64/python3.11/site-packages/ /usr/bin/python3 /build/promod3-3.2.1+ds/modelling/tests/test_alignment_fiddling.py" ... ---------------------------------------------------------------------- Ran 2 tests in 0.028s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 90%] Built target test_alignment_fiddling.py_run [ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -MF CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_all_atom_positions.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_all_atom_positions.cc ....[ 91%] Linking CXX executable ../../tests/core/test_suite_core cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 ..make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_suite_core make -f core/tests/CMakeFiles/test_suite_core_run.dir/build.make core/tests/CMakeFiles/test_suite_core_run.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/core/tests/CMakeFiles/test_suite_core_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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_amino_acid_atoms.cc.o -MF CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_amino_acid_atoms.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_amino_acid_atoms.cc [ 91%] running checks for module core cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/core/test_suite_core .Running 4 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_suite_core_run [ 91%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -MF CMakeFiles/test_suite_loop.dir/test_backbone.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_backbone.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_backbone.cc /build/promod3-3.2.1+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( | ^~~~~~~~~~~~~~~ .. ---------------------------------------------------------------------- Ran 2 tests in 6.214s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 91%] Built target test_sidechain_reconstruction.py_run [ 92%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -MF CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_forcefield.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_forcefield.cc [ 92%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -MF CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_hydrogens.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_hydrogens.cc [ 93%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_idx_handler.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_idx_handler.cc [ 93%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -MF CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_mm_system_creator.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_mm_system_creator.cc .[ 93%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_psipred_prediction.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_psipred_prediction.cc .[ 94%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -MF CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_sidechain_construction.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_sidechain_construction.cc [ 95%] Linking CXX executable ../../tests/sidechain/test_suite_sidechain cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 95%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/sidechain/tests/CMakeFiles/test_suite_sidechain_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 95%] running checks for module sidechain cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/sidechain/test_suite_sidechain Running 4 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 95%] Built target test_suite_sidechain_run [ 95%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -MF CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_torsion_sampler.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_torsion_sampler.cc [ 96%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=c++11 -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT loop/tests/CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -MF CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o.d -o CMakeFiles/test_suite_loop.dir/test_structuredb.cc.o -c /build/promod3-3.2.1+ds/loop/tests/test_structuredb.cc .....[ 96%] Building CXX object loop/tests/CMakeFiles/test_suite_loop.dir/tests.cc.o cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_UNIT_TEST_FRAMEWORK_DYN_LINK -I/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/loop/tests/tests.cc .[ 96%] Linking CXX executable ../../tests/scoring/test_suite_scoring cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 [ 96%] Linking CXX executable ../../tests/modelling/test_suite_modelling cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_modelling.so.3.2.1 ../../stage/lib64/libpromod3_scoring.so.3.2.1 ../../stage/lib64/libpromod3_sidechain.so.3.2.1 ../../stage/lib64/libpromod3_loop.so.3.2.1 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 96%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/scoring/tests/CMakeFiles/test_suite_scoring_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 97%] running checks for module scoring cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/scoring/test_suite_scoring make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 97%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/modelling/tests/CMakeFiles/test_suite_modelling_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] running checks for module modelling cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/modelling/test_suite_modelling ...Running 20 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_suite_scoring_run Running 7 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [ 98%] Built target test_suite_modelling_run ...[100%] Linking CXX executable ../../tests/loop/test_suite_loop cd /build/promod3-3.2.1+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/promod3-3.2.1+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 -Wl,-rpath,/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage/lib64 /usr/lib/x86_64-linux-gnu/libboost_unit_test_framework.so.1.74.0 ../../stage/lib64/libpromod3_loop.so.3.2.1 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 ../../stage/lib64/libpromod3_core.so.3.2.1 /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.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] 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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/loop/tests/CMakeFiles/test_suite_loop_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+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[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] running checks for module loop cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop && PROMOD3_ROOT=/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/stage /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/tests/loop/test_suite_loop ............ ---------------------------------------------------------------------- Ran 33 tests in 50.756s OK make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target test_close_gaps.py_run Running 68 test cases... *** No errors detected make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target test_suite_loop_run ........... ---------------------------------------------------------------------- Ran 15 tests in 86.480s 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[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target test_pipeline.py_run make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles/codetest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/codetest.dir/build.make CMakeFiles/codetest.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/codetest.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target codetest make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' cd /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[4]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/check.dir/build'. make[4]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' [100%] Built target check make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/promod3-3.2.1+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/promod3-3.2.1+ds' dh_auto_install cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/promod3-3.2.1\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/promod3-3.2.1+ds -B/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/config.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.2.1 -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.2 -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_core.so.3.2.1" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_core.so -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./check_io.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./cluster.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./dynamic_spatial_organizer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./export_helper.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./geom_base.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./geom_stems.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./message.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_sink.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./portable_binary_data_source.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./portable_binary_serializer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./runtime_profiling.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./superpose.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./enumerator.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./graph.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./tree.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./tetrahedral_polytope.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./graph_minimizer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/core/./eigen_types.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/_core.so -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/_core.so" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/helper.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/core/pm3argparse.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.2.1 -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.2 -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_loop.so.3.2.1" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_loop.so -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./all_atom_env.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./all_atom_positions.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./amino_acid_atoms.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./backbone.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./bb_trace_param.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./data_bag.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./dense_hash_table.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Up-to-date: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./dense_map.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./density_creator.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./forcefield_lookup.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./frag_db.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./fragger.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./hydrogen_rule_lookup.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./idx_handler.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./loop_object_loader.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./mm_system_creator.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./psipred_prediction.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./stem_geom.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./structure_db.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./torsion_sampler.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./ushort_vec.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_rule_lookup.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./sidechain_atom_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/loop/./structure_db_custom_types.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/_loop.so -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/_loop.so" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/loop/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_coil.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_extended.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/torsion_sampler_helical.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/frag_db.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/structure_db.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/loop_data/ff_lookup_charmm.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.2.1 -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.2 -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_scoring.so.3.2.1" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_scoring.so -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./backbone_score_base.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./backbone_overall_scorer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./scoring_object_loader.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./cb_packing_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./cbeta_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./reduced_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./reduced_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./clash_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./clash_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./density_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./hbond_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./hbond_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./ss_agreement_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./torsion_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_scoring_function.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./pairwise_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./constraint_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_score_base.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_overall_scorer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_interaction_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_packing_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./all_atom_clash_score.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/scoring/./scwrl3_energy_functions.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/_scoring.so -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/_scoring.so" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/scoring/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/cb_packing_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/cbeta_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/reduced_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/hbond_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/ss_agreement_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/torsion_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/aa_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/scoring_data/aa_packing_scorer.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.2.1 -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.2 -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so.3.2.1" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_sidechain.so -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./bb_dep_rotamer_lib.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./disulfid.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./frame.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_graph.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./particle.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring_base.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./particle_scoring.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_particle_scoring.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_particle_scoring.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./vina_particle_scoring.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_cruncher.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_density.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_group.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_id.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_entry.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lib_reader.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_connector.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./sidechain_object_loader.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./rotamer_lookup.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl4_rotamer_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./scwrl3_rotamer_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./vina_rotamer_constructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/sidechain/./subrotamer_optimizer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/_sidechain.so" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/sidechain/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/sidechain_data/lib.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/share/promod3/sidechain_data/bb_dep_lib.dat -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.2.1 -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.2 -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_modelling.so.3.2.1" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/libpromod3_modelling.so -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./extension_scheme.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./gap.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./gap_extender.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./model.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./all_atom_relaxer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./backbone_relaxer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./ccd.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./kic.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./loop_candidate.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_closer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_cooler.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_sampler.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./monte_carlo_scorer.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./rigid_blocks.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./score_container.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./scoring_weights.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_reconstructor.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./sidechain_env_listener.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./motif_finder.hh -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/include/promod3/modelling/./robin_hood.h -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_modelling.so -- Set runtime path of "/build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_modelling.so" to "" -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/__init__.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_closegaps.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_molprobity.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_pipeline.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_ring_punches.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_denovo.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_fragger_handle.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_reconstruct_sidechains.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_monte_carlo.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_mhandle_helper.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_alignment_fiddling.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/lib64/python3.11/site-packages/promod3/modelling/_raw_model.py -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/bin/pm -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/libexec/promod3/pm-build-model -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/libexec/promod3/pm-build-rawmodel -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/libexec/promod3/pm-help -- Installing: /build/promod3-3.2.1+ds/debian/tmp/usr/libexec/promod3/pm-build-sidechains make[2]: Leaving directory '/build/promod3-3.2.1+ds/obj-x86_64-linux-gnu' mv debian/tmp/usr/bin/pm debian/tmp/usr/bin/promod # See debian/README.Debian make[1]: Leaving directory '/build/promod3-3.2.1+ds' debian/rules override_dh_install-arch make[1]: Entering directory '/build/promod3-3.2.1+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-${PKG}3.2 usr/lib64/libpromod3_${PKG}.so.* usr/lib/x86_64-linux-gnu; \ done make[1]: Leaving directory '/build/promod3-3.2.1+ds' debian/rules override_dh_install-indep make[1]: Entering directory '/build/promod3-3.2.1+ds' dh_install rm -rf debian/tmp/usr/include/promod3 debian/tmp/usr/lib64 make[1]: Leaving directory '/build/promod3-3.2.1+ds' dh_installdocs dh_installchangelogs dh_python3 I: dh_python3 fs:483: renaming _modelling.so to _modelling.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _sidechain.so to _sidechain.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _scoring.so to _scoring.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _loop.so to _loop.cpython-311-x86_64-linux-gnu.so I: dh_python3 fs:483: renaming _core.so to _core.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 ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-promod3: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-promod3: substitution variable ${python3:Provides} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'libpromod3-core-dev' in '../libpromod3-core-dev_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.2-dbgsym' in '../libpromod3-core3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.2' in '../libpromod3-loop3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling-dev' in '../libpromod3-modelling-dev_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.2-dbgsym' in '../libpromod3-modelling3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.2' in '../libpromod3-scoring3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain-dev' in '../libpromod3-sidechain-dev_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.2-dbgsym' in '../libpromod3-sidechain3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'promod3-data' in '../promod3-data_3.2.1+ds-6_all.deb'. dpkg-deb: building package 'python3-promod3-dbgsym' in '../python3-promod3-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-core3.2' in '../libpromod3-core3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-sidechain3.2' in '../libpromod3-sidechain3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-modelling3.2' in '../libpromod3-modelling3.2_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring3.2-dbgsym' in '../libpromod3-scoring3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-loop3.2-dbgsym' in '../libpromod3-loop3.2-dbgsym_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-loop-dev' in '../libpromod3-loop-dev_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'promod3' in '../promod3_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'libpromod3-scoring-dev' in '../libpromod3-scoring-dev_3.2.1+ds-6_amd64.deb'. dpkg-deb: building package 'python3-promod3' in '../python3-promod3_3.2.1+ds-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../promod3_3.2.1+ds-6_amd64.buildinfo dpkg-genchanges --build=binary -O../promod3_3.2.1+ds-6_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: user script /srv/workspace/pbuilder/3094074/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3094074/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3094074 and its subdirectories I: Current time: Tue Jun 6 03:56:40 +14 2023 I: pbuilder-time-stamp: 1685973400