sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | macromoleculebuilder 3.2+dfsg-1 (amd64) Sun, 04 Oct 2020 22:07:56 +0000 | +==============================================================================+ Package: macromoleculebuilder Version: 3.2+dfsg-1 Source Version: 3.2+dfsg-1 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-f7cf63b0-392b-4dba-8a39-ec632daae41c' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup macromoleculebuilder_3.2+dfsg-1 sid amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup macromoleculebuilder_3.2+dfsg-1 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-s2pAqp/resolver-VpIuCk' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [146 kB] Get:2 http://localhost:3142/debian sid InRelease [146 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-04-0800.48.pdiff [1707 B] Get:5 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-04-1401.12.pdiff [13.4 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-04-2001.04.pdiff [14.1 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-04-2001.04.pdiff [14.1 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Get:8 http://localhost:3142/debian sid/main Sources 2020-10-04-0800.48.pdiff [4026 B] Get:9 http://localhost:3142/debian sid/main Sources 2020-10-04-1401.12.pdiff [12.1 kB] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-04-2001.04.pdiff [12.1 kB] Get:10 http://localhost:3142/debian sid/main Sources 2020-10-04-2001.04.pdiff [12.1 kB] Fetched 406 kB in 2s (163 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: netbase 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.9 kB of archives. After this operation, 2048 B disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 netbase all 6.2 [19.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.9 kB in 0s (0 B/s) (Reading database ... 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Configuration file '/etc/services' ==> Modified (by you or by a script) since installation. ==> Package distributor has shipped an updated version. ==> Using current old file as you requested. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/macromoleculebuilder_3.2+dfsg-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-s2pAqp/macromoleculebuilder-3.2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-s2pAqp' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: asciidoc-base, cmake, debhelper-compat (= 12), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev, build-essential, fakeroot Filtered Build-Depends: asciidoc-base, cmake, debhelper-compat (= 12), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [412 B] Get:5 copy:/<>/apt_archive ./ Packages [495 B] Fetched 1864 B in 0s (31.3 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file freeglut3 freeglut3-dev g++ g++-10 gcc gcc-10 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6 libblas-dev libblas3 libbrotli1 libbsd0 libc6-dev libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-dev libegl-mesa0 libegl1 libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgbm1 libgcc-10-dev libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgssapi-krb5-2 libice-dev libice6 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm10 libmagic-mgc libmagic1 libmmdb2-0 libncurses6 libnghttp2-14 libopengl-dev libopengl0 libopenmm-dev libopenmm7.5 libpciaccess0 libperl5.30 libpipeline1 libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsensors-config libsensors5 libseqan2-dev libsigsegv2 libsimbody-dev libsimbody3.6 libsimtkmolmodel-dev libsimtkmolmodel3.0 libsm-dev libsm6 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libvulkan1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi-dev libxi6 libxml2 libxml2-utils libxmu-dev libxmu-headers libxmu6 libxshmfence1 libxslt1.1 libxt-dev libxt6 libxxf86vm1 libz3-4 m4 man-db mime-support perl perl-modules-5.30 po-debconf procps python3 python3-minimal python3.8 python3.8-minimal sensible-utils x11-common x11proto-core-dev x11proto-dev x11proto-input-dev x11proto-xext-dev xorg-sgml-doctools xsltproc xtrans-dev Suggested packages: asciidoc-doc docbook-utils source-highlight autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make debian-keyring g++-multilib g++-10-multilib gcc-10-doc gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-10-multilib gcc-10-locales gettext-doc libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc glibc-doc git bzr krb5-doc krb5-user libice-doc pciutils lm-sensors libsm-doc libstdc++-10-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support Recommended packages: xmlto libalgorithm-merge-perl curl | wget | lynx ca-certificates libfile-fcntllock-perl liblocale-gettext-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev mesa-vulkan-drivers | vulkan-icd libmail-sendmail-perl psmisc The following NEW packages will be installed: asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file freeglut3 freeglut3-dev g++ g++-10 gcc gcc-10 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6 libblas-dev libblas3 libbrotli1 libbsd0 libc6-dev libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-dev libegl-mesa0 libegl1 libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgbm1 libgcc-10-dev libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgssapi-krb5-2 libice-dev libice6 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libllvm10 libmagic-mgc libmagic1 libmmdb2-0 libncurses6 libnghttp2-14 libopengl-dev libopengl0 libopenmm-dev libopenmm7.5 libpciaccess0 libperl5.30 libpipeline1 libprocps8 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsensors-config libsensors5 libseqan2-dev libsigsegv2 libsimbody-dev libsimbody3.6 libsimtkmolmodel-dev libsimtkmolmodel3.0 libsm-dev libsm6 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libvulkan1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi-dev libxi6 libxml2 libxml2-utils libxmu-dev libxmu-headers libxmu6 libxshmfence1 libxslt1.1 libxt-dev libxt6 libxxf86vm1 libz3-4 m4 man-db mime-support perl perl-modules-5.30 po-debconf procps python3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-main-dummy sensible-utils x11-common x11proto-core-dev x11proto-dev x11proto-input-dev x11proto-xext-dev xorg-sgml-doctools xsltproc xtrans-dev 0 upgraded, 181 newly installed, 0 to remove and 0 not upgraded. Need to get 139 MB of archives. After this operation, 575 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B] Get:2 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://localhost:3142/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB] Get:9 http://localhost:3142/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpython3.8-minimal amd64 3.8.6-1 [761 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.2.10-1 [96.9 kB] Get:13 http://localhost:3142/debian unstable/main amd64 python3.8-minimal amd64 3.8.6-1 [1863 kB] Get:14 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:15 http://localhost:3142/debian unstable/main amd64 mime-support all 3.64 [37.8 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libpython3.8-stdlib amd64 3.8.6-1 [1720 kB] Get:17 http://localhost:3142/debian unstable/main amd64 python3.8 amd64 3.8.6-1 [422 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:19 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libprocps8 amd64 2:3.3.16-5 [62.7 kB] Get:22 http://localhost:3142/debian unstable/main amd64 procps amd64 2:3.3.16-5 [262 kB] Get:23 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:26 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:27 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:28 http://localhost:3142/debian unstable/main amd64 asciidoc-common all 9.0.0~rc2-1 [286 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libxml2-utils amd64 2.9.10+dfsg-6 [108 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libxslt1.1 amd64 1.1.34-4 [239 kB] Get:33 http://localhost:3142/debian unstable/main amd64 xsltproc amd64 1.1.34-4 [124 kB] Get:34 http://localhost:3142/debian unstable/main amd64 asciidoc-base all 9.0.0~rc2-1 [135 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:36 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:37 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:38 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:39 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.2-4 [801 kB] Get:40 http://localhost:3142/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.17-1 [104 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libc6-dev amd64 2.31-3 [2395 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libasan6 amd64 10.2.0-13 [340 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 10.2.0-13 [134 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libgcc-10-dev amd64 10.2.0-13 [2327 kB] Get:46 http://localhost:3142/debian unstable/main amd64 gcc-10 amd64 10.2.0-13 [15.9 MB] Get:47 http://localhost:3142/debian unstable/main amd64 gcc amd64 4:10.2.0-1 [5196 B] Get:48 http://localhost:3142/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.0-13 [1738 kB] Get:49 http://localhost:3142/debian unstable/main amd64 g++-10 amd64 10.2.0-13 [8670 kB] Get:50 http://localhost:3142/debian unstable/main amd64 g++ amd64 4:10.2.0-1 [1644 B] Get:51 http://localhost:3142/debian unstable/main amd64 libdpkg-perl all 1.20.5 [1473 kB] Get:52 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.20.5 [1909 kB] Get:53 http://localhost:3142/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:54 http://localhost:3142/debian unstable/main amd64 cmake-data all 3.18.2-1 [1725 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libarchive13 amd64 3.4.3-2 [342 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2 [287 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.17-10 [64.6 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.17-10 [115 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.17-10 [366 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-10 [156 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.41.0-3 [74.0 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libpsl5 amd64 0.21.0-1.1 [55.3 kB] Get:64 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libcurl4 amd64 7.72.0-1 [336 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:68 http://localhost:3142/debian unstable/main amd64 librhash0 amd64 1.4.0-1 [124 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libuv1 amd64 1.39.0-1 [131 kB] Get:70 http://localhost:3142/debian unstable/main amd64 cmake amd64 3.18.2-1 [5596 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:72 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.2.1 [188 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:77 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libelf1 amd64 0.181-1 [164 kB] Get:79 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:80 http://localhost:3142/debian unstable/main amd64 libglib2.0-0 amd64 2.66.0-2 [1361 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:82 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:83 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:84 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:85 http://localhost:3142/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.25.2-1 [46.9 kB] Get:87 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.25.2-1 [86.8 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.6.12-1 [311 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.102-1 [14.5 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libdrm2 amd64 2.4.102-1 [41.5 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libglapi-mesa amd64 20.1.9-1 [70.4 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libx11-xcb1 amd64 2:1.6.12-1 [203 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libxcb-dri2-0 amd64 1.14-2 [103 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libxcb-dri3-0 amd64 1.14-2 [102 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libxcb-glx0 amd64 1.14-2 [118 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libxcb-present0 amd64 1.14-2 [101 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libxcb-sync1 amd64 1.14-2 [105 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:108 http://localhost:3142/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:109 http://localhost:3142/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.102-1 [28.2 kB] Get:110 http://localhost:3142/debian unstable/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libdrm-intel1 amd64 2.4.102-1 [70.4 kB] Get:112 http://localhost:3142/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.102-1 [26.5 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.102-1 [29.7 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:115 http://localhost:3142/debian unstable/main amd64 libz3-4 amd64 4.8.9-1 [6783 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libllvm10 amd64 1:10.0.1-6 [16.6 MB] Get:117 http://localhost:3142/debian unstable/main amd64 libsensors-config all 1:3.6.0-2 [32.0 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-2 [53.1 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libvulkan1 amd64 1.2.148.1-1 [102 kB] Get:120 http://localhost:3142/debian unstable/main amd64 libgl1-mesa-dri amd64 20.1.9-1 [9544 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libglx-mesa0 amd64 20.1.9-1 [187 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get:125 http://localhost:3142/debian unstable/main amd64 freeglut3 amd64 2.8.1-6 [125 kB] Get:126 http://localhost:3142/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get:127 http://localhost:3142/debian unstable/main amd64 x11proto-dev all 2020.1-1 [594 kB] Get:128 http://localhost:3142/debian unstable/main amd64 x11proto-core-dev all 2020.1-1 [3404 B] Get:129 http://localhost:3142/debian unstable/main amd64 libxau-dev amd64 1:1.0.8-1+b2 [23.1 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:131 http://localhost:3142/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:133 http://localhost:3142/debian unstable/main amd64 libxcb1-dev amd64 1.14-2 [176 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libx11-dev amd64 2:1.6.12-1 [842 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libglx-dev amd64 1.3.2-1 [16.3 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libgl-dev amd64 1.3.2-1 [100 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libwayland-server0 amd64 1.18.0-2~exp1.1 [34.4 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libgbm1 amd64 20.1.9-1 [76.2 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libwayland-client0 amd64 1.18.0-2~exp1.1 [26.9 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libxcb-xfixes0 amd64 1.14-2 [105 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libegl-mesa0 amd64 20.1.9-1 [144 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libegl1 amd64 1.3.2-1 [34.8 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libegl-dev amd64 1.3.2-1 [19.6 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libgles1 amd64 1.3.2-1 [12.6 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libgles2 amd64 1.3.2-1 [17.7 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libgles-dev amd64 1.3.2-1 [50.3 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libopengl0 amd64 1.3.2-1 [31.5 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libopengl-dev amd64 1.3.2-1 [5876 B] Get:149 http://localhost:3142/debian unstable/main amd64 libglvnd-dev amd64 1.3.2-1 [13.9 kB] Get:150 http://localhost:3142/debian unstable/main amd64 libgl1-mesa-dev amd64 20.1.9-1 [50.3 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libglu1-mesa amd64 9.0.1-1 [168 kB] Get:152 http://localhost:3142/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.1-1 [207 kB] Get:153 http://localhost:3142/debian unstable/main amd64 x11proto-xext-dev all 2020.1-1 [3404 B] Get:154 http://localhost:3142/debian unstable/main amd64 libxext-dev amd64 2:1.3.3-1+b2 [107 kB] Get:155 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+20 [252 kB] Get:156 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:157 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:158 http://localhost:3142/debian unstable/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:159 http://localhost:3142/debian unstable/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get:160 http://localhost:3142/debian unstable/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get:161 http://localhost:3142/debian unstable/main amd64 libxt-dev amd64 1:1.2.0-1 [407 kB] Get:162 http://localhost:3142/debian unstable/main amd64 freeglut3-dev amd64 2.8.1-6 [179 kB] Get:163 http://localhost:3142/debian unstable/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get:164 http://localhost:3142/debian unstable/main amd64 libblas-dev amd64 3.9.0-3 [161 kB] Get:165 http://localhost:3142/debian unstable/main amd64 libgfortran5 amd64 10.2.0-13 [728 kB] Get:166 http://localhost:3142/debian unstable/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get:167 http://localhost:3142/debian unstable/main amd64 liblapack-dev amd64 3.9.0-3 [4247 kB] Get:168 http://localhost:3142/debian unstable/main amd64 libmmdb2-0 amd64 2.0.5-1 [333 kB] Get:169 http://localhost:3142/debian unstable/main amd64 libopenmm7.5 amd64 7.4.0.491.gac5a8f71+dfsg-1 [806 kB] Get:170 http://localhost:3142/debian unstable/main amd64 libopenmm-dev amd64 7.4.0.491.gac5a8f71+dfsg-1 [148 kB] Get:171 http://localhost:3142/debian unstable/main amd64 libseqan2-dev all 2.4.0+dfsg-12 [1220 kB] Get:172 http://localhost:3142/debian unstable/main amd64 libxfixes-dev amd64 1:5.0.3-2 [24.1 kB] Get:173 http://localhost:3142/debian unstable/main amd64 x11proto-input-dev all 2020.1-1 [3412 B] Get:174 http://localhost:3142/debian unstable/main amd64 libxi-dev amd64 2:1.7.10-1 [242 kB] Get:175 http://localhost:3142/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:176 http://localhost:3142/debian unstable/main amd64 libxmu-headers all 2:1.1.2-2 [51.9 kB] Get:177 http://localhost:3142/debian unstable/main amd64 libxmu-dev amd64 2:1.1.2-2+b3 [66.3 kB] Get:178 http://localhost:3142/debian unstable/main amd64 libsimbody3.6 amd64 3.6.1+dfsg-7 [3218 kB] Get:179 http://localhost:3142/debian unstable/main amd64 libsimbody-dev amd64 3.6.1+dfsg-7 [2726 kB] Get:180 http://localhost:3142/debian unstable/main amd64 libsimtkmolmodel3.0 amd64 3.0~svn842-2 [532 kB] Get:181 http://localhost:3142/debian unstable/main amd64 libsimtkmolmodel-dev amd64 3.0~svn842-2 [1858 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 139 MB in 6s (23.7 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10509 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3+b1_amd64.deb ... Unpacking bsdextrautils (2.36-3+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../05-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... 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Setting up libssl1.1:amd64 (1.1.1g-1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.8-minimal (3.8.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13299 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.8.2-3_amd64.deb ... Unpacking python3-minimal (3.8.2-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libpython3.8-stdlib:amd64. Preparing to unpack .../libpython3.8-stdlib_3.8.6-1_amd64.deb ... Unpacking libpython3.8-stdlib:amd64 (3.8.6-1) ... Selecting previously unselected package python3.8. Preparing to unpack .../python3.8_3.8.6-1_amd64.deb ... Unpacking python3.8 (3.8.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Selecting previously unselected package libsimbody-dev:amd64. Preparing to unpack .../160-libsimbody-dev_3.6.1+dfsg-7_amd64.deb ... Unpacking libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Selecting previously unselected package libsimtkmolmodel3.0:amd64. Preparing to unpack .../161-libsimtkmolmodel3.0_3.0~svn842-2_amd64.deb ... Unpacking libsimtkmolmodel3.0:amd64 (3.0~svn842-2) ... Selecting previously unselected package libsimtkmolmodel-dev:amd64. Preparing to unpack .../162-libsimtkmolmodel-dev_3.0~svn842-2_amd64.deb ... Unpacking libsimtkmolmodel-dev:amd64 (3.0~svn842-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../163-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libwayland-server0:amd64 (1.18.0-2~exp1.1) ... Setting up libx11-xcb1:amd64 (2:1.6.12-1) ... Setting up libpciaccess0:amd64 (0.16-1) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libpsl5:amd64 (0.21.0-1.1) ... Setting up perl-modules-5.30 (5.30.3-4) ... Setting up mime-support (3.64) ... Setting up bsdextrautils (2.36-3+b1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-4) ... Setting up libmmdb2-0:amd64 (2.0.5-1) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libglib2.0-0:amd64 (2.66.0-2) ... No schema files found: doing nothing. Setting up libglvnd0:amd64 (1.3.2-1) ... Setting up libbrotli1:amd64 (1.0.9-2) ... Setting up x11-common (1:7.7+20) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up libsensors-config (1:3.6.0-2) ... Setting up libopenmm7.5 (7.4.0.491.gac5a8f71+dfsg-1) ... Setting up libnghttp2-14:amd64 (1.41.0-3) ... Setting up libmagic1:amd64 (1:5.38-5) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-5) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libopenmm-dev (7.4.0.491.gac5a8f71+dfsg-1) ... Setting up libopengl0:amd64 (1.3.2-1) ... Setting up libfakeroot:amd64 (1.25.2-1) ... Setting up libasan6:amd64 (10.2.0-13) ... Setting up libkrb5support0:amd64 (1.17-10) ... Setting up libseqan2-dev (2.4.0+dfsg-12) ... Setting up fakeroot (1.25.2-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up asciidoc-common (9.0.0~rc2-1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libz3-4:amd64 (4.8.9-1) ... Setting up libblas3:amd64 (3.9.0-3) ... 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 libuv1:amd64 (1.39.0-1) ... Setting up libgles2:amd64 (1.3.2-1) ... Setting up libx11-data (2:1.6.12-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20200918-1) ... Setting up libgles1:amd64 (1.3.2-1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-10) ... Setting up libsensors5:amd64 (1:3.6.0-2) ... Setting up libk5crypto3:amd64 (1.17-10) ... Setting up libglapi-mesa:amd64 (20.1.9-1) ... Setting up libgfortran5:amd64 (10.2.0-13) ... Setting up libvulkan1:amd64 (1.2.148.1-1) ... Setting up libubsan1:amd64 (10.2.0-13) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up librhash0:amd64 (1.4.0-1) ... Setting up libcrypt-dev:amd64 (1:4.4.17-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libperl5.30:amd64 (5.30.3-4) ... Setting up libc6-dev:amd64 (2.31-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up cmake-data (3.18.2-1) ... Setting up libkrb5-3:amd64 (1.17-10) ... Setting up libopengl-dev:amd64 (1.3.2-1) ... Setting up libpython3.8-stdlib:amd64 (3.8.6-1) ... Setting up python3.8 (3.8.6-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libdrm-common (2.4.102-1) ... Setting up libelf1:amd64 (0.181-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6) ... Setting up libprocps8:amd64 (2:3.3.16-5) ... Setting up libblas-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libjsoncpp1:amd64 (1.7.4-3.1) ... Setting up libpython3-stdlib:amd64 (3.8.2-3) ... Setting up libwayland-client0:amd64 (1.18.0-2~exp1.1) ... Setting up x11proto-dev (2020.1-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3) ... 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 (1.14-2) ... Setting up libxcb-xfixes0:amd64 (1.14-2) ... Setting up libxau-dev:amd64 (1:1.0.8-1+b2) ... Setting up libice-dev:amd64 (2:1.0.10-1) ... Setting up libarchive13:amd64 (3.4.3-2) ... Setting up libxcb-glx0:amd64 (1.14-2) ... Setting up libgcc-10-dev:amd64 (10.2.0-13) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-3) ... Setting up libllvm10:amd64 (1:10.0.1-6) ... Setting up libxcb-present0:amd64 (1.14-2) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up perl (5.30.3-4) ... Setting up libxcb-sync1:amd64 (1.14-2) ... Setting up x11proto-core-dev (2020.1-1) ... Setting up liblapack-dev:amd64 (3.9.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-10) ... Setting up x11proto-input-dev (2020.1-1) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up gcc-10 (10.2.0-13) ... Setting up libdpkg-perl (1.20.5) ... Setting up autoconf (2.69-11.1) ... Setting up libxcb-dri2-0:amd64 (1.14-2) ... Setting up x11proto-xext-dev (2020.1-1) ... Setting up libdrm2:amd64 (2.4.102-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up procps (2:3.3.16-5) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libxslt1.1:amd64 (1.1.34-4) ... Setting up libcurl4:amd64 (7.72.0-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libx11-6:amd64 (2:1.6.12-1) ... Setting up libxml2-utils (2.9.10+dfsg-6) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.102-1) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.14-2) ... Setting up libdrm-nouveau2:amd64 (2.4.102-1) ... Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-10-dev:amd64 (10.2.0-13) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up libxcb1-dev:amd64 (1.14-2) ... Setting up g++-10 (10.2.0-13) ... Setting up libgbm1:amd64 (20.1.9-1) ... Setting up libtool (2.4.6-14) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdrm-radeon1:amd64 (2.4.102-1) ... Setting up libdebhelper-perl (13.2.1) ... Setting up libdrm-intel1:amd64 (2.4.102-1) ... Setting up libgl1-mesa-dri:amd64 (20.1.9-1) ... Setting up xsltproc (1.1.34-4) ... Setting up libx11-dev:amd64 (2:1.6.12-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gcc (4:10.2.0-1) ... Setting up dpkg-dev (1.20.5) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up asciidoc-base (9.0.0~rc2-1) ... Setting up libegl-mesa0:amd64 (20.1.9-1) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libxext-dev:amd64 (2:1.3.3-1+b2) ... Setting up g++ (4:10.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libegl1:amd64 (1.3.2-1) ... Setting up cmake (3.18.2-1) ... Setting up build-essential (12.8) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up libxmu-headers (2:1.1.2-2) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libglx-mesa0:amd64 (20.1.9-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up po-debconf (1.0.21) ... Setting up libxfixes-dev:amd64 (1:5.0.3-2) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libxt-dev:amd64 (1:1.2.0-1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up libglx-dev:amd64 (1.3.2-1) ... Setting up libglu1-mesa:amd64 (9.0.1-1) ... Setting up libxi-dev:amd64 (2:1.7.10-1) ... Setting up libgl-dev:amd64 (1.3.2-1) ... Setting up freeglut3:amd64 (2.8.1-6) ... Setting up libegl-dev:amd64 (1.3.2-1) ... Setting up libxmu-dev:amd64 (2:1.1.2-2+b3) ... Setting up libglu1-mesa-dev:amd64 (9.0.1-1) ... Setting up libsimbody3.6:amd64 (3.6.1+dfsg-7) ... Setting up libgles-dev:amd64 (1.3.2-1) ... Setting up libsimtkmolmodel3.0:amd64 (3.0~svn842-2) ... Setting up libsimtkmolmodel-dev:amd64 (3.0~svn842-2) ... Setting up libglvnd-dev:amd64 (1.3.2-1) ... Setting up libgl1-mesa-dev:amd64 (20.1.9-1) ... Setting up freeglut3-dev:amd64 (2.8.1-6) ... Setting up libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-13 gcc-10_10.2.0-13 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-13 libstdc++6_10.2.0-13 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 asciidoc-base_9.0.0~rc2-1 asciidoc-common_9.0.0~rc2-1 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-common_2.35.1-1 binutils-x86-64-linux-gnu_2.35.1-1 bsdextrautils_2.36-3+b1 bsdutils_1:2.36-3+b1 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.2-1 cmake-data_3.18.2-1 coreutils_8.32-4+b1 cpp_4:10.2.0-1 cpp-10_10.2.0-13 cpp-7_7.5.0-6 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 eatmydata_105-9 fakeroot_1.25.2-1 fdisk_2.36-3+b1 file_1:5.38-5 findutils_4.7.0-1 freeglut3_2.8.1-6 freeglut3-dev_2.8.1-6 g++_4:10.2.0-1 g++-10_10.2.0-13 gcc_4:10.2.0-1 gcc-10_10.2.0-13 gcc-10-base_10.2.0-13 gcc-7-base_7.5.0-6 gcc-8-base_8.4.0-4 gcc-9-base_9.3.0-18 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan4_7.5.0-6 libasan6_10.2.0-13 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.35.1-1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3+b1 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3 libc-dev-bin_2.31-3 libc6_2.31-3 libc6-dev_2.31-3 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-13 libcilkrts5_7.5.0-6 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-1 libctf0_2.35.1-1 libcurl4_7.72.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5 libdrm-amdgpu1_2.4.102-1 libdrm-common_2.4.102-1 libdrm-intel1_2.4.102-1 libdrm-nouveau2_2.4.102-1 libdrm-radeon1_2.4.102-1 libdrm2_2.4.102-1 libeatmydata1_105-9 libedit2_3.1-20191231-1 libegl-dev_1.3.2-1 libegl-mesa0_20.1.9-1 libegl1_1.3.2-1 libelf1_0.181-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.2-1 libfdisk1_2.36-3+b1 libffi6_3.2.1-9 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgbm1_20.1.9-1 libgcc-10-dev_10.2.0-13 libgcc-s1_10.2.0-13 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm5_1.14.1-6+b1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-13 libgl-dev_1.3.2-1 libgl1_1.3.2-1 libgl1-mesa-dev_20.1.9-1 libgl1-mesa-dri_20.1.9-1 libglapi-mesa_20.1.9-1 libgles-dev_1.3.2-1 libgles1_1.3.2-1 libgles2_1.3.2-1 libglib2.0-0_2.66.0-2 libglu1-mesa_9.0.1-1 libglu1-mesa-dev_9.0.1-1 libglvnd-dev_1.3.2-1 libglvnd0_1.3.2-1 libglx-dev_1.3.2-1 libglx-mesa0_20.1.9-1 libglx0_1.3.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.6-2 libice-dev_2:1.0.10-1 libice6_2:1.0.10-1 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.2.0-13 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.53+dfsg-1 libldap-common_2.4.53+dfsg-1 libllvm10_1:10.0.1-6 liblsan0_10.2.0-13 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmmdb2-0_2.0.5-1 libmount1_2.36-3+b1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpx2_8.4.0-4 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libopengl-dev_1.3.2-1 libopengl0_1.3.2-1 libopenmm-dev_7.4.0.491.gac5a8f71+dfsg-1 libopenmm7.5_7.4.0.491.gac5a8f71+dfsg-1 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.16-1 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.26_5.26.2-7+b1 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 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libudev1_246.6-1 libunistring2_0.9.10-4 libuuid1_2.36-3+b1 libuv1_1.39.0-1 libvulkan1_1.2.148.1-1 libwayland-client0_1.18.0-2~exp1.1 libwayland-server0_1.18.0-2~exp1.1 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libx11-dev_2:1.6.12-1 libx11-xcb1_2:1.6.12-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb-dri2-0_1.14-2 libxcb-dri3-0_1.14-2 libxcb-glx0_1.14-2 libxcb-present0_1.14-2 libxcb-sync1_1.14-2 libxcb-xfixes0_1.14-2 libxcb1_1.14-2 libxcb1-dev_1.14-2 libxdamage1_1:1.1.5-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1+b2 libxext6_2:1.3.3-1+b2 libxfixes-dev_1:5.0.3-2 libxfixes3_1:5.0.3-2 libxi-dev_2:1.7.10-1 libxi6_2:1.7.10-1 libxml2_2.9.10+dfsg-6 libxml2-utils_2.9.10+dfsg-6 libxmu-dev_2:1.1.2-2+b3 libxmu-headers_2:1.1.2-2 libxmu6_2:1.1.2-2+b3 libxshmfence1_1.3-1 libxslt1.1_1.1.34-4 libxt-dev_1:1.2.0-1 libxt6_1:1.2.0-1 libxxf86vm1_1:1.1.4-1+b2 libz3-4_4.8.9-1 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.10-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macromoleculebuilder Binary: libmmblib-dev, libmmblib3.2, mmb, mmb-common Architecture: any all Version: 3.2+dfsg-1 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/rnatoolbox Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/debichem-team/macromoleculebuilder Vcs-Git: https://salsa.debian.org/debichem-team/macromoleculebuilder.git Build-Depends: asciidoc-base, cmake, debhelper-compat (= 12), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev Package-List: libmmblib-dev deb libdevel optional arch=any libmmblib3.2 deb libs optional arch=any mmb deb science optional arch=any mmb-common deb science optional arch=all Checksums-Sha1: 88b9198cf490b04d9a779feaa40b2234f350fee7 2473540 macromoleculebuilder_3.2+dfsg.orig.tar.xz 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disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network macromoleculebuilder_3.2+dfsg-1 sid amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network macromoleculebuilder_3.2+dfsg-1 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-f7cf63b0-392b-4dba-8a39-ec632daae41c SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c3941047 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 3.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building macromoleculebuilder using existing ./macromoleculebuilder_3.2+dfsg.orig.tar.xz dpkg-source: warning: ignoring deletion of file parameterization/build/Makefile.bak, use --include-removal to override dpkg-source: warning: ignoring deletion of file parameterization/src/generate-base-pair-transform.cpp.bak, use --include-removal to override dpkg-source: info: building macromoleculebuilder in macromoleculebuilder_3.2+dfsg-1.debian.tar.xz dpkg-source: info: building macromoleculebuilder in macromoleculebuilder_3.2+dfsg-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ -DOpenMM_INCLUDE_DIR=/usr/include \ -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0" 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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DOpenMM_INCLUDE_DIR=/usr/include "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0" .. -- The C compiler identification is GNU 10.2.0 -- The CXX compiler identification is GNU 10.2.0 -- 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 -- 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 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake --color= Scanning dependencies of target MMBlib make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMBlib.dir/src/Utils.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Utils.cpp.o -c /<>/src/Utils.cpp [ 6%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o [ 10%] Building CXX object CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o -c /<>/src/BiopolymerClass.cpp /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o -c /<>/src/AtomSpringContainer.cpp [ 13%] Building CXX object CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o -c /<>/src/UnitCellParameters.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/src/AtomSpringContainer.cpp:12: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/UnitCellParameters.cpp: In member function ‘const double UnitCellParameters::angleInRange(double)’: /<>/src/UnitCellParameters.cpp:165:2: warning: control reaches end of non-void function [-Wreturn-type] 165 | } | ^ /<>/src/UnitCellParameters.cpp: In member function ‘const bool UnitCellParameters::exitIfNotValid() const’: /<>/src/UnitCellParameters.cpp:270:1: warning: control reaches end of non-void function [-Wreturn-type] 270 | } | ^ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/src/BiopolymerClass.cpp:13: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClass::setRenumberPdbResidues(bool)’: /<>/src/BiopolymerClass.cpp:1067:5: warning: no return statement in function returning non-void [-Wreturn-type] 1067 | } | ^ [ 17%] Building CXX object CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o -c /<>/src/DisplacementContainer.cpp /<>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClassContainer::setRenumberPdbResidues(bool)’: /<>/src/BiopolymerClass.cpp:4725:1: warning: no return statement in function returning non-void [-Wreturn-type] 4725 | } | ^ In file included from /<>/src/Utils.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/Utils.cpp: In function ‘int ValidateNonNegativeInt(int)’: /<>/src/Utils.cpp:526:1: warning: control reaches end of non-void function [-Wreturn-type] 526 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::validateBiopolymerType() const’: /<>/src/BiopolymerClass.cpp:356:1: warning: control reaches end of non-void function [-Wreturn-type] 356 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘SimTK::String BiopolymerClass::getBiopolymerTypeAsString()’: /<>/src/BiopolymerClass.cpp:1062:1: warning: control reaches end of non-void function [-Wreturn-type] 1062 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::validateAtomPathName(SimTK::Compound::AtomPathName)’: /<>/src/BiopolymerClass.cpp:1133:1: warning: control reaches end of non-void function [-Wreturn-type] 1133 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘const SimTK::ResidueInfo::Index BiopolymerClass::getResidueIndex(ResidueID)’: /<>/src/BiopolymerClass.cpp:1529:1: warning: control reaches end of non-void function [-Wreturn-type] 1529 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘SimTK::String BiopolymerClass::getRepresentativeAtomName()’: /<>/src/BiopolymerClass.cpp:1552:1: warning: control reaches end of non-void function [-Wreturn-type] 1552 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘double BiopolymerClass::getRepresentativeAtomMassThreshold()’: /<>/src/BiopolymerClass.cpp:1569:1: warning: control reaches end of non-void function [-Wreturn-type] 1569 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::initializeBiopolymer(SimTK::String, SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, double, std::vector, double, double, std::vector)’: /<>/src/BiopolymerClass.cpp:2749:1: warning: control reaches end of non-void function [-Wreturn-type] 2749 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::getBiopolymerClassIndex(SimTK::String)’: /<>/src/BiopolymerClass.cpp:2850:1: warning: control reaches end of non-void function [-Wreturn-type] 2850 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass& BiopolymerClassContainer::updBiopolymerClass(int)’: /<>/src/BiopolymerClass.cpp:2867:1: warning: control reaches end of non-void function [-Wreturn-type] 2867 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClassContainer::validateChainID(SimTK::String)’: /<>/src/BiopolymerClass.cpp:3038:1: warning: control reaches end of non-void function [-Wreturn-type] 3038 | } | ^ /<>/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClassContainer::residueID(std::map, const char*, SimTK::String)’: /<>/src/BiopolymerClass.cpp:4174:1: warning: control reaches end of non-void function [-Wreturn-type] 4174 | } | ^ [ 20%] Building CXX object CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o -c /<>/src/MobilizerContainer.cpp [ 24%] Building CXX object CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o -c /<>/src/MoleculeContainer.cpp In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/include/DisplacementContainer.h:14, from /<>/src/DisplacementContainer.cpp:12: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/DisplacementContainer.cpp: In member function ‘Displacement& DisplacementContainer::updDisplacement(SimTK::String)’: /<>/src/DisplacementContainer.cpp:41:1: warning: control reaches end of non-void function [-Wreturn-type] 41 | }; | ^ [ 27%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o -c /<>/src/DensityContainer.cpp [ 31%] Building CXX object CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o -c /<>/src/BasePairContainer.cpp In file included from /<>/src/MobilizerContainer.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/ConstraintContainer.h:14, from /<>/include/MoleculeContainer.h:9, from /<>/src/MoleculeContainer.cpp:3: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/MoleculeContainer.cpp: In member function ‘SimTK::Compound CompoundObjectMapContainer::fetchCompound(SimTK::String)’: /<>/src/MoleculeContainer.cpp:73:1: warning: control reaches end of non-void function [-Wreturn-type] 73 | } | ^ /<>/src/MoleculeContainer.cpp: In member function ‘SimTK::Biotype CompoundObjectMapContainer::fetchBiotype(SimTK::String)’: /<>/src/MoleculeContainer.cpp:92:1: warning: control reaches end of non-void function [-Wreturn-type] 92 | } | ^ /<>/src/MoleculeContainer.cpp: In member function ‘const SimTK::Element CompoundObjectMapContainer::fetchElement(SimTK::String)’: /<>/src/MoleculeContainer.cpp:220:1: warning: control reaches end of non-void function [-Wreturn-type] 220 | } | ^ /<>/src/MoleculeContainer.cpp: In member function ‘SimTK::Compound::SingleAtom CompoundObjectMapContainer::fetchSingleAtom(SimTK::String, SimTK::Compound::AtomName&, SimTK::String, SimTK::Angle)’: /<>/src/MoleculeContainer.cpp:244:1: warning: control reaches end of non-void function [-Wreturn-type] 244 | } | ^ /<>/src/MoleculeContainer.cpp: In member function ‘bool MoleculeClassContainer::hasChainID(SimTK::String)’: /<>/src/MoleculeContainer.cpp:722:1: warning: control reaches end of non-void function [-Wreturn-type] 722 | } | ^ [ 34%] Building CXX object CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o -c /<>/src/ContactContainer.cpp [ 37%] Building CXX object CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o -c /<>/src/ConstraintContainer.cpp In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/include/DensityContainer.h:14, from /<>/src/DensityContainer.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/include/BasePairContainer.h:14, from /<>/src/BasePairContainer.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/BasePairContainer.cpp: In member function ‘bool BasePairContainer::hasWatsonCrickCisPair(SimTK::String, ResidueID)’: /<>/src/BasePairContainer.cpp:184:1: warning: control reaches end of non-void function [-Wreturn-type] 184 | } | ^ /<>/src/BasePairContainer.cpp: In member function ‘const BaseInteraction BasePairContainer::getWatsonCrickCisPair(SimTK::String, ResidueID)’: /<>/src/BasePairContainer.cpp:206:1: warning: control reaches end of non-void function [-Wreturn-type] 206 | } // of method | ^ /<>/src/BasePairContainer.cpp: In member function ‘const ResidueID BasePairContainer::getWatsonCrickCisPairingResidue(SimTK::String, ResidueID)’: /<>/src/BasePairContainer.cpp:223:1: warning: control reaches end of non-void function [-Wreturn-type] 223 | } | ^ /<>/src/BasePairContainer.cpp: In member function ‘const SimTK::String BasePairContainer::getWatsonCrickCisPairingChain(SimTK::String, ResidueID)’: /<>/src/BasePairContainer.cpp:237:1: warning: control reaches end of non-void function [-Wreturn-type] 237 | } | ^ /<>/src/BasePairContainer.cpp: In member function ‘const ResidueID BasePairContainer::getLastWatsonCrickCisPairingResidueOfRun(SimTK::String, ResidueID, BiopolymerClassContainer&)’: /<>/src/BasePairContainer.cpp:289:1: warning: control reaches end of non-void function [-Wreturn-type] 289 | } // of getLastWatsonCrickCisPairingResidueOfRun | ^ [ 41%] Building CXX object CMakeFiles/MMBlib.dir/src/Repel.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/Repel.cpp.o -c /<>/src/Repel.cpp [ 44%] Building CXX object CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o -c /<>/src/MonoAtoms.cpp In file included from /<>/src/ContactContainer.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/ConstraintContainer.h:14, from /<>/src/ConstraintContainer.cpp:10: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 48%] Building CXX object CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o -c /<>/src/ParameterReader.cpp [ 51%] Building CXX object CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o -c /<>/src/BaseInteractionParameterReader.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/PeriodicScrubber.h:16, from /<>/include/Repel.h:21, from /<>/src/Repel.cpp:12: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’: /<>/src/Repel.cpp:127:49: note: ‘#pragma message: USE_OPENMM is defined’ 127 | #pragma message ("USE_OPENMM is defined") | ^ In file included from /<>/src/MonoAtoms.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/MonoAtoms.cpp: In member function ‘const int MonoAtoms::getResidueIndex(ResidueID)’: /<>/src/MonoAtoms.cpp:153:1: warning: control reaches end of non-void function [-Wreturn-type] 153 | } | ^ /<>/src/MonoAtoms.cpp: In member function ‘MonoAtoms MonoAtomsContainer::getMonoAtoms(SimTK::String)’: /<>/src/MonoAtoms.cpp:277:1: warning: control reaches end of non-void function [-Wreturn-type] 277 | } | ^ [ 55%] Building CXX object CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o -c /<>/src/TetherForce.cpp [ 58%] Building CXX object CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /<>/src/BiopolymerClassTwoTransformForces.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/src/ParameterReader.cpp:17: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/BaseInteractionParameterReader.h:22, from /<>/src/BaseInteractionParameterReader.cpp:16: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 62%] Building CXX object CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o -c /<>/src/WaterDroplet.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/TetherForce.h:20, from /<>/src/TetherForce.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/BiopolymerClassTwoTransformForces.h:18, from /<>/src/BiopolymerClassTwoTransformForces.cpp:10: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 65%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o -c /<>/src/DensityMap.cpp In file included from /<>/include/WaterDroplet.h:16, from /<>/src/WaterDroplet.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 68%] Building CXX object CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o -c /<>/src/DensityForce.cpp /<>/src/WaterDroplet.cpp: In member function ‘WaterDroplet WaterDropletContainer::getWaterDroplet(std::string)’: /<>/src/WaterDroplet.cpp:108:1: warning: control reaches end of non-void function [-Wreturn-type] 108 | } | ^ /<>/src/WaterDroplet.cpp: In member function ‘WaterDroplet& WaterDropletContainer::updWaterDroplet(std::string)’: /<>/src/WaterDroplet.cpp:120:1: warning: control reaches end of non-void function [-Wreturn-type] 120 | } | ^ [ 72%] Building CXX object CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /<>/src/ElectrostaticPotentialGridForce.cpp [ 75%] Building CXX object CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o -c /<>/src/ErrorManager.cpp /<>/src/ErrorManager.cpp: In member function ‘ErrorManager& ErrorManager::operator=(const ErrorManager&)’: /<>/src/ErrorManager.cpp:25:1: warning: no return statement in function returning non-void [-Wreturn-type] 24 | _buffer << em._buffer.rdbuf(); +++ |+ return *this; 25 | } | ^ [ 79%] Building CXX object CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /<>/src/PeriodicPdbAndEnergyWriter.cpp In file included from /<>/src/DensityMap.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/DensityForce.h:20, from /<>/src/DensityForce.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ /<>/src/DensityMap.cpp: In member function ‘GridPoint& DensityMap::updGridPoint(GridIndices)’: /<>/src/DensityMap.cpp:127:5: warning: control reaches end of non-void function [-Wreturn-type] 127 | } | ^ /<>/src/DensityMap.cpp: In member function ‘SimTK::Vec3 DensityMap::calcInterpolatedFirstQuadrantGradient(GridPoint&, SimTK::Vec3) const’: /<>/src/DensityMap.cpp:1448:1: warning: control reaches end of non-void function [-Wreturn-type] 1448 | } | ^ [ 82%] Building CXX object CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o -c /<>/src/NTC_PARAMETER_READER.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/ElectrostaticPotentialGridForce.h:20, from /<>/src/ElectrostaticPotentialGridForce.cpp:11: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/PeriodicPdbAndEnergyWriter.h:13, from /<>/src/PeriodicPdbAndEnergyWriter.cpp:15: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 86%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o -c /<>/src/NtCClassContainer.cpp [ 89%] Building CXX object CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o /usr/bin/c++ -DMMBlib_EXPORTS -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fPIC -DMMB_BUILDING_SHARED_LIBRARY -o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -c /<>/src/NtCForces.cpp In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/include/NtC_Class_Container.h:14, from /<>/src/NTC_PARAMETER_READER.cpp:16: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:18, from /<>/src/NtCClassContainer.cpp:12: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/NtCForces.h:19, from /<>/src/NtCForces.cpp:10: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [ 93%] Linking CXX shared library libMMBlib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/MMBlib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -shared -Wl,-soname,libMMBlib.so.3.2 -o libMMBlib.so.3.2 CMakeFiles/MMBlib.dir/src/Utils.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMBlib.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMBlib.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMBlib.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMBlib.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMBlib.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMBlib.dir/src/DensityContainer.cpp.o CMakeFiles/MMBlib.dir/src/BasePairContainer.cpp.o CMakeFiles/MMBlib.dir/src/ContactContainer.cpp.o CMakeFiles/MMBlib.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMBlib.dir/src/Repel.cpp.o CMakeFiles/MMBlib.dir/src/MonoAtoms.cpp.o CMakeFiles/MMBlib.dir/src/ParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMBlib.dir/src/TetherForce.cpp.o CMakeFiles/MMBlib.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMBlib.dir/src/WaterDroplet.cpp.o CMakeFiles/MMBlib.dir/src/DensityMap.cpp.o CMakeFiles/MMBlib.dir/src/DensityForce.cpp.o CMakeFiles/MMBlib.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMBlib.dir/src/ErrorManager.cpp.o CMakeFiles/MMBlib.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMBlib.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMBlib.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMBlib.dir/src/NtCForces.cpp.o -L/usr/lib/x86_64-linux-gnu64 -L/<>/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/<>/obj-x86_64-linux-gnu: -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -ldl -lrt -lm /usr/bin/cmake -E cmake_symlink_library libMMBlib.so.3.2 libMMBlib.so.3.2 libMMBlib.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target MMBlib make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= Scanning dependencies of target MMB make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 96%] Building CXX object CMakeFiles/MMB.dir/src/RNABuilder.cpp.o /usr/bin/c++ -I/<>/include -I/usr/include/openmm -I/usr/include/openmm/reference -isystem /usr/include/simbody -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -o CMakeFiles/MMB.dir/src/RNABuilder.cpp.o -c /<>/src/RNABuilder.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/src/RNABuilder.cpp:15: /<>/include/Utils.h:33:70: note: ‘#pragma message: using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined’ 33 | #pragma message ("using OpenMM::Vec3: USE_OPENMM_REALVEC NOT defined") | ^ [100%] Linking CXX executable MMB /usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1 /usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -Wl,-z,relro -rdynamic CMakeFiles/MMB.dir/src/RNABuilder.cpp.o -o MMB -L/usr/lib/x86_64-linux-gnu64 -L/<>/obj-x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu64:/<>/obj-x86_64-linux-gnu: libMMBlib.so.3.2 -lSimTKmolmodel /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lOpenMM -llapack -lblas -ldl -lrt -lblas -llapack -lblas -llapack -lpthread -lm -ldl -lrt make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target MMB make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_testroot dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/macromoleculebuilder-3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/MMBlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMBlib.dir/build.make CMakeFiles/MMBlib.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/MMBlib.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 93%] Built target MMBlib make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/MMB.dir/build'. make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target MMB make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/lib/libMMBlib.so.3.2 -- Set runtime path of "/<>/debian/tmp/usr/lib/libMMBlib.so.3.2" to "" -- Installing: /<>/debian/tmp/usr/lib/libMMBlib.so -- Installing: /<>/debian/tmp/usr/bin/MMB -- Set runtime path of "/<>/debian/tmp/usr/bin/MMB" to "" -- Installing: /<>/debian/tmp/usr/share/MMB/parameters.csv -- Installing: /<>/debian/tmp/usr/scripts -- Installing: /<>/debian/tmp/usr/scripts/renumber.pl -- Installing: 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/<>/debian/tmp/usr/examples/antibody-antigen.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.TetRB.scanning.dat -- Installing: /<>/debian/tmp/usr/examples/commands.A_N.32.G.dat -- Installing: /<>/debian/tmp/usr/examples/commands.disulphide-bonded-cysteines.dat -- Installing: /<>/debian/tmp/usr/examples/commands.protein-homology-modeling.dat -- Installing: /<>/debian/tmp/usr/examples/1UAO-disre-simple.txt -- Installing: /<>/debian/tmp/usr/examples/commands.tRNA-fitting.dat -- Installing: /<>/debian/tmp/usr/examples/commands.GlnBP-thermal-exploration.dat -- Installing: /<>/debian/tmp/usr/examples/commands.benzene.dat -- Installing: /<>/debian/tmp/usr/examples/1GID.shifted.pdb -- Installing: /<>/debian/tmp/usr/examples/.commands.GNRA-NtC.dat.swp -- Installing: /<>/debian/tmp/usr/examples/commands.NMR.dat -- Installing: /<>/debian/tmp/usr/examples/TetRB.scanning.pdb -- Installing: /<>/debian/tmp/usr/examples/protein-template.pdb -- Installing: /<>/debian/tmp/usr/examples/1UAO.atoms-renamed.pdb -- Installing: /<>/debian/tmp/usr/examples/5MRC.GNRA.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.TetR_threading_TUT.dat -- Installing: /<>/debian/tmp/usr/examples/commands.template-docking.dat -- Installing: /<>/debian/tmp/usr/examples/6TNA.short.pdb -- Installing: /<>/debian/tmp/usr/examples/tRNA.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.DNA-helix.dat -- Installing: /<>/debian/tmp/usr/examples/commands.hairpin-short.dat -- Installing: /<>/debian/tmp/usr/examples/parameters.csv -- Installing: /<>/debian/tmp/usr/examples/1mlc.DEF.pdb -- Installing: /<>/debian/tmp/usr/examples/1WDN.short.pdb -- Installing: /<>/debian/tmp/usr/examples/TetR.pdb -- Installing: /<>/debian/tmp/usr/examples/1BA2.aligned.pdb -- Installing: /<>/debian/tmp/usr/examples/1ARJ.short.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.GNRA-NtC.dat -- Installing: /<>/debian/tmp/usr/examples/commands.antibody-antigen.flexible-interfaces.dat -- Installing: /<>/debian/tmp/usr/examples/1mlb.AB.pdb -- Installing: /<>/debian/tmp/usr/examples/1FC2.C-to-A.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.A_N.32.N.dat -- Installing: /<>/debian/tmp/usr/examples/commands.long-chain-ID.dat -- Installing: /<>/debian/tmp/usr/examples/commands.singlebasepair.dat -- Installing: /<>/debian/tmp/usr/examples/1GGG.short.pdb -- Installing: /<>/debian/tmp/usr/examples/commands.protein-morphing.dat -- Installing: /<>/debian/tmp/usr/examples/commands.TAR.dat make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install dh_install -plibmmblib3.2 debian/tmp/usr/lib/libMMBlib.so.* usr/lib/x86_64-linux-gnu dh_install -plibmmblib-dev debian/tmp/usr/lib/libMMBlib.so usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc a2x: ERROR: "xmllint" --nonet --noout --valid "/<>/debian/tmp/MMB.1.xml" returned non-zero exit status 4 make[1]: *** [debian/rules:22: override_dh_installman] Error 1 make[1]: Leaving directory '/<>' make: *** [debian/rules:9: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-10-04T22:12:03Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 491360 Build-Time: 187 Distribution: sid Fail-Stage: build Host Architecture: amd64 Install-Time: 48 Job: /srv/debomatic/incoming/macromoleculebuilder_3.2+dfsg-1.dsc Machine Architecture: amd64 Package: macromoleculebuilder Package-Time: 247 Source-Version: 3.2+dfsg-1 Space: 491360 Status: attempted Version: 3.2+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-10-04T22:12:03Z Build needed 00:04:07, 491360k disk space