sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir.einval.org +==============================================================================+ | molmodel 3.0.113.gd05a5b6-2 (amd64) Mon, 22 Aug 2022 04:03:28 +0000 | +==============================================================================+ Package: molmodel Version: 3.0.113.gd05a5b6-2 Source Version: 3.0.113.gd05a5b6-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-a55b5efb-04c7-4e4d-9f5c-104f974b2e29' with '<>' I: NOTICE: Log filtering will replace 'build/molmodel-UMVc9t/resolver-TOphdp' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian sid InRelease [192 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB] Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index Get:4 http://mirror.einval.org/debian sid/main amd64 Packages [9349 kB] Get:5 http://mirror.einval.org/debian sid/main Sources [9892 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [9197 kB] Fetched 28.6 MB in 8s (3804 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser libdebconfclient0 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 181 kB of archives. After this operation, 53.2 kB of additional disk space will be used. Get:1 http://mirror.einval.org/debian sid/main arm64 adduser all 3.127 [130 kB] Get:2 http://mirror.einval.org/debian sid/main arm64 libdebconfclient0 arm64 0.264 [51.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 181 kB in 0s (6467 kB/s) (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 ... 12473 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.127_all.deb ... adduser.conf with unknown checksum (probably locally changed) encountered. You can continue after answering the dpkg configuration file question. Unpacking adduser (3.127) over (3.123) ... Setting up adduser (3.127) ... Configuration file '/etc/adduser.conf' ==> File on system created by you or by a script. ==> File also in package provided by package maintainer. ==> Using current old file as you requested. (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 ... 12474 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.264_arm64.deb ... Unpacking libdebconfclient0:arm64 (0.264) over (0.263) ... Setting up libdebconfclient0:arm64 (0.264) ... Processing triggers for libc-bin (2.34-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'molmodel' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/molmodel.git Please use: git clone https://salsa.debian.org/debichem-team/molmodel.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 8560 kB of source archives. Get:1 http://mirror.einval.org/debian sid/main molmodel 3.0.113.gd05a5b6-2 (dsc) [2182 B] Get:2 http://mirror.einval.org/debian sid/main molmodel 3.0.113.gd05a5b6-2 (tar) [8555 kB] Get:3 http://mirror.einval.org/debian sid/main molmodel 3.0.113.gd05a5b6-2 (diff) [3116 B] Fetched 8560 kB in 0s (41.3 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/molmodel-UMVc9t/molmodel-3.0.113.gd05a5b6' with '<>' I: NOTICE: Log filtering will replace 'build/molmodel-UMVc9t' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64 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 [438 B] Get:5 copy:/<>/apt_archive ./ Packages [525 B] Fetched 1920 B in 0s (47.0 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: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dmsetup dpkg-cross dwz emacsen-common file freeglut3:amd64 freeglut3-dev:amd64 g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gemmi-dev:amd64 gettext gettext-base groff-base intltool-debian libapparmor1 libarchive-zip-perl libarchive13 libargon2-1 libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libbrotli1 libbsd0 libbsd0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcryptsetup12 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdevmapper1.02.1 libdrm-amdgpu1:amd64 libdrm-common libdrm-nouveau2:amd64 libdrm-radeon1:amd64 libdrm2:amd64 libedit2:amd64 libegl-dev:amd64 libegl-mesa0:amd64 libegl1:amd64 libelf1 libelf1:amd64 libexpat1 libexpat1:amd64 libfdisk1 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgbm1:amd64 libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64 libgl1-mesa-dev:amd64 libgl1-mesa-dri:amd64 libglapi-mesa:amd64 libgles-dev:amd64 libgles1:amd64 libgles2:amd64 libglu1-mesa:amd64 libglu1-mesa-dev:amd64 libglvnd-core-dev:amd64 libglvnd-dev:amd64 libglvnd0:amd64 libglx-dev:amd64 libglx-mesa0:amd64 libglx0:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libice-dev:amd64 libice6:amd64 libicu71 libicu71:amd64 libio-string-perl libip4tc2 libitm1:amd64 libitm1-amd64-cross libjson-c5 libjsoncpp25 libk5crypto3:amd64 libkeyutils1:amd64 libkmod2 libkrb5-3:amd64 libkrb5support0:amd64 liblapack-dev:amd64 liblapack3:amd64 libldap-2.5-0 libllvm14:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma5:amd64 libmagic-mgc libmagic1 libmd0 libmd0:amd64 libmmdb2-0:amd64 libmmdb2-dev:amd64 libncurses6 libncursesw6 libnghttp2-14 libnsl-dev:amd64 libnsl2:amd64 libopengl-dev:amd64 libopengl0:amd64 libpipeline1 libprocps8 libpsl5 libpthread-stubs0-dev libpthread-stubs0-dev:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:amd64 libsimbody-dev:amd64 libsimbody3.6:amd64 libsm-dev:amd64 libsm6:amd64 libssh2-1 libssl3:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsystemd-shared libtinfo6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libuuid1:amd64 libuv1 libwayland-client0:amd64 libwayland-server0:amd64 libx11-6 libx11-6:amd64 libx11-data libx11-dev libx11-dev:amd64 libx11-xcb1:amd64 libxau-dev libxau-dev:amd64 libxau6 libxau6:amd64 libxcb-dri2-0:amd64 libxcb-dri3-0:amd64 libxcb-glx0:amd64 libxcb-present0:amd64 libxcb-shm0:amd64 libxcb-sync1:amd64 libxcb-xfixes0:amd64 libxcb1 libxcb1:amd64 libxcb1-dev libxcb1-dev:amd64 libxdmcp-dev libxdmcp-dev:amd64 libxdmcp6 libxdmcp6:amd64 libxext-dev:amd64 libxext6:amd64 libxfixes-dev:amd64 libxfixes3:amd64 libxi-dev:amd64 libxi6:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:amd64 libxmu-dev:amd64 libxmu-headers libxmu6:amd64 libxshmfence1:amd64 libxt-dev:amd64 libxt6:amd64 libxxf86vm1:amd64 libyaml-perl libz3-4:amd64 libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf procps sensible-utils systemd tao-pegtl-dev ucf x11-common x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g:amd64 zlib1g-dev:amd64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc ninja-build cmake-format gcc-12-locales cpp-doc dh-make binutils-multiarch g++-12-multilib-x86-64-linux-gnu gcc-12-doc gcc-12-multilib-x86-64-linux-gnu manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 krb5-doc:amd64 krb5-user:amd64 libice-doc:amd64 lm-sensors lm-sensors:amd64 libsm-doc:amd64 libstdc++-12-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libx11-doc:amd64 libxcb-doc libxcb-doc:amd64 libxext-doc:amd64 libxt-doc:amd64 libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved libfido2-1 libtss2-esys-3.0.2-0 libtss2-mu0 libtss2-rc0 policykit-1 Recommended packages: curl | wget | lynx libidn2-0:amd64 ca-certificates libarchive-cpio-perl krb5-locales:amd64 libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev uuid-runtime:amd64 libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc default-dbus-system-bus | dbus-system-bus systemd-timesyncd | time-daemon The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-12-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config crossbuild-essential-amd64 debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dmsetup dpkg-cross dwz emacsen-common file freeglut3:amd64 freeglut3-dev:amd64 g++-12-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-12-base:amd64 gcc-12-cross-base gcc-12-x86-64-linux-gnu gcc-12-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gemmi-dev:amd64 gettext gettext-base groff-base intltool-debian libapparmor1 libarchive-zip-perl libarchive13 libargon2-1 libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libbrotli1 libbsd0 libbsd0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcryptsetup12 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdevmapper1.02.1 libdrm-amdgpu1:amd64 libdrm-common libdrm-nouveau2:amd64 libdrm-radeon1:amd64 libdrm2:amd64 libedit2:amd64 libegl-dev:amd64 libegl-mesa0:amd64 libegl1:amd64 libelf1 libelf1:amd64 libexpat1 libexpat1:amd64 libfdisk1 libffi8:amd64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgbm1:amd64 libgcc-12-dev:amd64 libgcc-12-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64 libgl1-mesa-dev:amd64 libgl1-mesa-dri:amd64 libglapi-mesa:amd64 libgles-dev:amd64 libgles1:amd64 libgles2:amd64 libglu1-mesa:amd64 libglu1-mesa-dev:amd64 libglvnd-core-dev:amd64 libglvnd-dev:amd64 libglvnd0:amd64 libglx-dev:amd64 libglx-mesa0:amd64 libglx0:amd64 libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libice-dev:amd64 libice6:amd64 libicu71 libicu71:amd64 libio-string-perl libip4tc2 libitm1:amd64 libitm1-amd64-cross libjson-c5 libjsoncpp25 libk5crypto3:amd64 libkeyutils1:amd64 libkmod2 libkrb5-3:amd64 libkrb5support0:amd64 liblapack-dev:amd64 liblapack3:amd64 libldap-2.5-0 libllvm14:amd64 liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross liblzma5:amd64 libmagic-mgc libmagic1 libmd0 libmd0:amd64 libmmdb2-0:amd64 libmmdb2-dev:amd64 libncurses6 libncursesw6 libnghttp2-14 libnsl-dev:amd64 libnsl2:amd64 libopengl-dev:amd64 libopengl0:amd64 libpipeline1 libprocps8 libpsl5 libpthread-stubs0-dev libpthread-stubs0-dev:amd64 libquadmath0:amd64 libquadmath0-amd64-cross librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:amd64 libsimbody-dev:amd64 libsimbody3.6:amd64 libsm-dev:amd64 libsm6:amd64 libssh2-1 libssl3:amd64 libstdc++-12-dev:amd64 libstdc++-12-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libsystemd-shared libtinfo6:amd64 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libuuid1:amd64 libuv1 libwayland-client0:amd64 libwayland-server0:amd64 libx11-6 libx11-6:amd64 libx11-data libx11-dev libx11-dev:amd64 libx11-xcb1:amd64 libxau-dev libxau-dev:amd64 libxau6 libxau6:amd64 libxcb-dri2-0:amd64 libxcb-dri3-0:amd64 libxcb-glx0:amd64 libxcb-present0:amd64 libxcb-shm0:amd64 libxcb-sync1:amd64 libxcb-xfixes0:amd64 libxcb1 libxcb1:amd64 libxcb1-dev libxcb1-dev:amd64 libxdmcp-dev libxdmcp-dev:amd64 libxdmcp6 libxdmcp6:amd64 libxext-dev:amd64 libxext6:amd64 libxfixes-dev:amd64 libxfixes3:amd64 libxi-dev:amd64 libxi6:amd64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:amd64 libxmu-dev:amd64 libxmu-headers libxmu6:amd64 libxshmfence1:amd64 libxt-dev:amd64 libxt6:amd64 libxxf86vm1:amd64 libyaml-perl libz3-4:amd64 libzstd1:amd64 linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db po-debconf procps sbuild-build-depends-main-dummy:amd64 sensible-utils systemd tao-pegtl-dev ucf x11-common x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 244 newly installed, 0 to remove and 0 not upgraded. Need to get 327 MB of archives. After this operation, 1263 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://mirror.einval.org/debian sid/main arm64 libargon2-1 arm64 0~20171227-0.3 [18.9 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 dmsetup arm64 2:1.02.185-1 [85.8 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-1 [126 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 libjson-c5 arm64 0.16-1 [42.7 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 libcryptsetup12 arm64 2:2.5.0-2 [239 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libfdisk1 arm64 2.38.1-1 [239 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libkmod2 arm64 30+20220630-3 [56.0 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 libapparmor1 arm64 3.0.7-1 [102 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libip4tc2 arm64 1.8.8-1 [34.3 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 libsystemd-shared arm64 251.4-1 [1523 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 systemd arm64 251.4-1 [2708 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b2 [18.9 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libncurses6 arm64 6.3+20220423-2 [92.9 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.3+20220423-2 [121 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libprocps8 arm64 2:3.3.17-7+b1 [62.5 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 procps arm64 2:3.3.17-7+b1 [497 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.41-4 [295 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.41-4 [124 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.41-4 [66.9 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-8 [173 kB] Get:23 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-8 [882 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.38.1-1 [145 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.6-2 [37.3 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.10.2-2 [1393 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB] Get:29 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.19-1 [280 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:33 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-8 [510 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libicu71 arm64 71.1-3 [9046 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.14+dfsg-1+b1 [640 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libarchive13 arm64 3.6.0-1 [327 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b4 [270 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-7 [39.0 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libsasl2-2 arm64 2.1.28+dfsg-7 [76.5 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libldap-2.5-0 arm64 2.5.12+dfsg-2+b1 [214 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libnghttp2-14 arm64 1.48.0-2 [79.4 kB] Get:42 http://mirror.einval.org/debian sid/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libcurl4 arm64 7.84.0-2 [338 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.8-1 [94.6 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 dh-elpa-helper all 2.0.10 [11.3 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 emacsen-common all 3.0.4 [19.3 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 cmake-data all 3.24.1-1 [2018 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 cmake arm64 3.24.1-1 [5728 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 gcc-12-x86-64-linux-gnu-base arm64 12.1.0-7cross1 [208 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 cpp-12-x86-64-linux-gnu arm64 12.1.0-7cross1 [54.4 MB] Get:56 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:12.1.0-3 [17.1 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.38.90.20220713-2 [5493 kB] Get:59 http://mirror.einval.org/debian sid/main amd64 gcc-12-cross-base all 12.1.0-8cross1 [203 kB] Get:60 http://mirror.einval.org/debian sid/main amd64 libgcc-s1-amd64-cross all 12.1.0-8cross1 [50.2 kB] Get:61 http://mirror.einval.org/debian sid/main amd64 libgomp1-amd64-cross all 12.1.0-8cross1 [114 kB] Get:62 http://mirror.einval.org/debian sid/main amd64 libitm1-amd64-cross all 12.1.0-8cross1 [25.6 kB] Get:63 http://mirror.einval.org/debian sid/main amd64 libatomic1-amd64-cross all 12.1.0-8cross1 [9048 B] Get:64 http://mirror.einval.org/debian sid/main amd64 libasan8-amd64-cross all 12.1.0-8cross1 [2193 kB] Get:65 http://mirror.einval.org/debian sid/main amd64 liblsan0-amd64-cross all 12.1.0-8cross1 [968 kB] Get:66 http://mirror.einval.org/debian sid/main amd64 libtsan2-amd64-cross all 12.1.0-8cross1 [2197 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.34-3cross1 [1505 kB] Get:68 http://mirror.einval.org/debian sid/main amd64 libstdc++6-amd64-cross all 12.1.0-8cross1 [571 kB] Get:69 http://mirror.einval.org/debian sid/main amd64 libubsan1-amd64-cross all 12.1.0-8cross1 [882 kB] Get:70 http://mirror.einval.org/debian sid/main amd64 libquadmath0-amd64-cross all 12.1.0-8cross1 [144 kB] Get:71 http://mirror.einval.org/debian sid/main amd64 libgcc-12-dev-amd64-cross all 12.1.0-8cross1 [2437 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 gcc-12-x86-64-linux-gnu arm64 12.1.0-7cross1 [61.8 MB] Get:73 http://mirror.einval.org/debian sid/main arm64 gcc-x86-64-linux-gnu arm64 4:12.1.0-3 [1456 B] Get:74 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 5.18.16-1cross1 [1740 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.34-3cross1 [1891 kB] Get:76 http://mirror.einval.org/debian sid/main amd64 libstdc++-12-dev-amd64-cross all 12.1.0-8cross1 [2026 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 g++-12-x86-64-linux-gnu arm64 12.1.0-7cross1 [58.6 MB] Get:78 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:12.1.0-3 [1176 B] Get:79 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB] Get:80 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-2 [21.0 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1 [326 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.27-1 [17.3 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B] Get:93 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.9 [195 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.7-4 [526 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-3 [10.4 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.13.0-1 [15.8 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.187-1 [178 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-8 [1262 kB] Get:103 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:104 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:105 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.9 [1070 kB] Get:106 http://mirror.einval.org/debian sid/main amd64 gcc-12-base amd64 12.1.0-8 [208 kB] Get:107 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 12.1.0-8 [50.3 kB] Get:108 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.34-4 [2765 kB] Get:109 http://mirror.einval.org/debian sid/main amd64 libglvnd0 amd64 1.4.0-1 [51.0 kB] Get:110 http://mirror.einval.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:111 http://mirror.einval.org/debian sid/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:112 http://mirror.einval.org/debian sid/main amd64 libbsd0 amd64 0.11.6-1 [114 kB] Get:113 http://mirror.einval.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:114 http://mirror.einval.org/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:115 http://mirror.einval.org/debian sid/main arm64 libx11-data all 2:1.8.1-2 [308 kB] Get:116 http://mirror.einval.org/debian sid/main amd64 libx11-6 amd64 2:1.8.1-2 [772 kB] Get:117 http://mirror.einval.org/debian sid/main arm64 libdrm-common all 2.4.112-3 [15.6 kB] Get:118 http://mirror.einval.org/debian sid/main amd64 libdrm2 amd64 2.4.112-3 [45.8 kB] Get:119 http://mirror.einval.org/debian sid/main amd64 libexpat1 amd64 2.4.8-1 [109 kB] Get:120 http://mirror.einval.org/debian sid/main amd64 libglapi-mesa amd64 22.2.0~rc2-1 [75.6 kB] Get:121 http://mirror.einval.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.1-2 [203 kB] Get:122 http://mirror.einval.org/debian sid/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:123 http://mirror.einval.org/debian sid/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:124 http://mirror.einval.org/debian sid/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:125 http://mirror.einval.org/debian sid/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:126 http://mirror.einval.org/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:127 http://mirror.einval.org/debian sid/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:128 http://mirror.einval.org/debian sid/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:129 http://mirror.einval.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1 [53.1 kB] Get:130 http://mirror.einval.org/debian sid/main amd64 libxfixes3 amd64 1:6.0.0-1 [22.4 kB] Get:131 http://mirror.einval.org/debian sid/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:132 http://mirror.einval.org/debian sid/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:133 http://mirror.einval.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.112-3 [29.6 kB] Get:134 http://mirror.einval.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.112-3 [27.9 kB] Get:135 http://mirror.einval.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.112-3 [30.6 kB] Get:136 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-4.1 [92.7 kB] Get:137 http://mirror.einval.org/debian sid/main amd64 libelf1 amd64 0.187-1 [179 kB] Get:138 http://mirror.einval.org/debian sid/main amd64 libtinfo6 amd64 6.3+20220423-2 [351 kB] Get:139 http://mirror.einval.org/debian sid/main amd64 libedit2 amd64 3.1-20210910-1 [97.5 kB] Get:140 http://mirror.einval.org/debian sid/main amd64 libffi8 amd64 3.4.2-4 [24.7 kB] Get:141 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 12.1.0-8 [614 kB] Get:142 http://mirror.einval.org/debian sid/main amd64 libicu71 amd64 71.1-3 [9218 kB] Get:143 http://mirror.einval.org/debian sid/main amd64 liblzma5 amd64 5.2.5-2.1 [168 kB] Get:144 http://mirror.einval.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1+b1 [708 kB] Get:145 http://mirror.einval.org/debian sid/main amd64 libz3-4 amd64 4.8.12-1+b1 [6997 kB] Get:146 http://mirror.einval.org/debian sid/main amd64 libllvm14 amd64 1:14.0.6-2 [21.9 MB] Get:147 http://mirror.einval.org/debian sid/main arm64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:148 http://mirror.einval.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:149 http://mirror.einval.org/debian sid/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [275 kB] Get:150 http://mirror.einval.org/debian sid/main amd64 libgl1-mesa-dri amd64 22.2.0~rc2-1 [7114 kB] Get:151 http://mirror.einval.org/debian sid/main amd64 libglx-mesa0 amd64 22.2.0~rc2-1 [188 kB] Get:152 http://mirror.einval.org/debian sid/main amd64 libglx0 amd64 1.4.0-1 [33.7 kB] Get:153 http://mirror.einval.org/debian sid/main amd64 libgl1 amd64 1.4.0-1 [90.9 kB] Get:154 http://mirror.einval.org/debian sid/main amd64 libxi6 amd64 2:1.8-1 [84.0 kB] Get:155 http://mirror.einval.org/debian sid/main amd64 freeglut3 amd64 2.8.1-6 [125 kB] Get:156 http://mirror.einval.org/debian sid/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get:157 http://mirror.einval.org/debian sid/main arm64 x11proto-dev all 2022.1-1 [599 kB] Get:158 http://mirror.einval.org/debian sid/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get:159 http://mirror.einval.org/debian sid/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:160 http://mirror.einval.org/debian sid/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:161 http://mirror.einval.org/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:162 http://mirror.einval.org/debian sid/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get:163 http://mirror.einval.org/debian sid/main amd64 libx11-dev amd64 2:1.8.1-2 [848 kB] Get:164 http://mirror.einval.org/debian sid/main amd64 libglx-dev amd64 1.4.0-1 [16.6 kB] Get:165 http://mirror.einval.org/debian sid/main amd64 libgl-dev amd64 1.4.0-1 [101 kB] Get:166 http://mirror.einval.org/debian sid/main amd64 libglvnd-core-dev amd64 1.4.0-1 [14.2 kB] Get:167 http://mirror.einval.org/debian sid/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get:168 http://mirror.einval.org/debian sid/main amd64 libgbm1 amd64 22.2.0~rc2-1 [78.3 kB] Get:169 http://mirror.einval.org/debian sid/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get:170 http://mirror.einval.org/debian sid/main amd64 libegl-mesa0 amd64 22.2.0~rc2-1 [149 kB] Get:171 http://mirror.einval.org/debian sid/main amd64 libegl1 amd64 1.4.0-1 [35.1 kB] Get:172 http://mirror.einval.org/debian sid/main amd64 libegl-dev amd64 1.4.0-1 [20.2 kB] Get:173 http://mirror.einval.org/debian sid/main amd64 libgles1 amd64 1.4.0-1 [12.9 kB] Get:174 http://mirror.einval.org/debian sid/main amd64 libgles2 amd64 1.4.0-1 [18.2 kB] Get:175 http://mirror.einval.org/debian sid/main amd64 libgles-dev amd64 1.4.0-1 [50.7 kB] Get:176 http://mirror.einval.org/debian sid/main amd64 libopengl0 amd64 1.4.0-1 [31.9 kB] Get:177 http://mirror.einval.org/debian sid/main amd64 libopengl-dev amd64 1.4.0-1 [6220 B] Get:178 http://mirror.einval.org/debian sid/main amd64 libglvnd-dev amd64 1.4.0-1 [5972 B] Get:179 http://mirror.einval.org/debian sid/main amd64 libgl1-mesa-dev amd64 22.2.0~rc2-1 [54.8 kB] Get:180 http://mirror.einval.org/debian sid/main amd64 libglu1-mesa amd64 9.0.2-1 [172 kB] Get:181 http://mirror.einval.org/debian sid/main amd64 libglu1-mesa-dev amd64 9.0.2-1 [209 kB] Get:182 http://mirror.einval.org/debian sid/main amd64 libxext-dev amd64 2:1.3.4-1 [107 kB] Get:183 http://mirror.einval.org/debian sid/main arm64 x11-common all 1:7.7+23 [252 kB] Get:184 http://mirror.einval.org/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:185 http://mirror.einval.org/debian sid/main amd64 libuuid1 amd64 2.38.1-1 [86.1 kB] Get:186 http://mirror.einval.org/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:187 http://mirror.einval.org/debian sid/main amd64 libxt6 amd64 1:1.2.1-1 [189 kB] Get:188 http://mirror.einval.org/debian sid/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get:189 http://mirror.einval.org/debian sid/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get:190 http://mirror.einval.org/debian sid/main amd64 libxt-dev amd64 1:1.2.1-1 [408 kB] Get:191 http://mirror.einval.org/debian sid/main amd64 freeglut3-dev amd64 2.8.1-6 [179 kB] Get:192 http://mirror.einval.org/debian sid/main amd64 gemmi-dev amd64 0.5.6+ds-1 [400 kB] Get:193 http://mirror.einval.org/debian sid/main amd64 libasan8 amd64 12.1.0-8 [2194 kB] Get:194 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 12.1.0-8 [9320 B] Get:195 http://mirror.einval.org/debian sid/main amd64 libblas3 amd64 3.10.1-2 [156 kB] Get:196 http://mirror.einval.org/debian sid/main amd64 libblas-dev amd64 3.10.1-2 [164 kB] Get:197 http://mirror.einval.org/debian sid/main arm64 libmd0 arm64 1.0.4-2 [29.4 kB] Get:198 http://mirror.einval.org/debian sid/main arm64 libbsd0 arm64 0.11.6-1 [112 kB] Get:199 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 5.18.16-1 [1617 kB] Get:200 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.28-2 [89.3 kB] Get:201 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.28-2 [118 kB] Get:202 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.5-2 [75.7 kB] Get:203 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.20-1 [65.7 kB] Get:204 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.20-1 [111 kB] Get:205 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-1 [15.7 kB] Get:206 http://mirror.einval.org/debian sid/main amd64 libssl3 amd64 3.0.5-2 [2030 kB] Get:207 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.20-1 [363 kB] Get:208 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20-1 [166 kB] Get:209 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:210 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:211 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:212 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:213 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.34-4 [1894 kB] Get:214 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 12.1.0-8 [116 kB] Get:215 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 12.1.0-8 [26.1 kB] Get:216 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 12.1.0-8 [969 kB] Get:217 http://mirror.einval.org/debian sid/main amd64 libtsan2 amd64 12.1.0-8 [2197 kB] Get:218 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 12.1.0-8 [883 kB] Get:219 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 12.1.0-8 [145 kB] Get:220 http://mirror.einval.org/debian sid/main amd64 libgcc-12-dev amd64 12.1.0-8 [2437 kB] Get:221 http://mirror.einval.org/debian sid/main amd64 libgfortran5 amd64 12.1.0-8 [792 kB] Get:222 http://mirror.einval.org/debian sid/main amd64 liblapack3 amd64 3.10.1-2 [2202 kB] Get:223 http://mirror.einval.org/debian sid/main amd64 liblapack-dev amd64 3.10.1-2 [4317 kB] Get:224 http://mirror.einval.org/debian sid/main amd64 libmmdb2-0 amd64 2.0.22-1 [338 kB] Get:225 http://mirror.einval.org/debian sid/main amd64 libmmdb2-dev amd64 2.0.22-1 [92.9 kB] Get:226 http://mirror.einval.org/debian sid/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get:227 http://mirror.einval.org/debian sid/main amd64 libxfixes-dev amd64 1:6.0.0-1 [24.4 kB] Get:228 http://mirror.einval.org/debian sid/main amd64 libxi-dev amd64 2:1.8-1 [245 kB] Get:229 http://mirror.einval.org/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get:230 http://mirror.einval.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get:231 http://mirror.einval.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get:232 http://mirror.einval.org/debian sid/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get:233 http://mirror.einval.org/debian sid/main arm64 libx11-6 arm64 2:1.8.1-2 [750 kB] Get:234 http://mirror.einval.org/debian sid/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB] Get:235 http://mirror.einval.org/debian sid/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get:236 http://mirror.einval.org/debian sid/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get:237 http://mirror.einval.org/debian sid/main arm64 libx11-dev arm64 2:1.8.1-2 [828 kB] Get:238 http://mirror.einval.org/debian sid/main arm64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get:239 http://mirror.einval.org/debian sid/main amd64 libxmu-dev amd64 2:1.1.3-3 [65.9 kB] Get:240 http://mirror.einval.org/debian sid/main amd64 libsimbody3.6 amd64 3.6.1+dfsg-7 [3218 kB] Get:241 http://mirror.einval.org/debian sid/main amd64 libsimbody-dev amd64 3.6.1+dfsg-7 [2726 kB] Get:242 http://mirror.einval.org/debian sid/main amd64 libstdc++-12-dev amd64 12.1.0-8 [2045 kB] Get:243 http://mirror.einval.org/debian sid/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get:244 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-4.1 [193 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 327 MB in 5s (65.3 MB/s) Selecting previously unselected package libargon2-1:arm64. (Reading database ... 12474 files and directories currently installed.) Preparing to unpack .../000-libargon2-1_0~20171227-0.3_arm64.deb ... Unpacking libargon2-1:arm64 (0~20171227-0.3) ... Selecting previously unselected package dmsetup. Preparing to unpack .../001-dmsetup_2%3a1.02.185-1_arm64.deb ... Unpacking dmsetup (2:1.02.185-1) ... Selecting previously unselected package libdevmapper1.02.1:arm64. Preparing to unpack .../002-libdevmapper1.02.1_2%3a1.02.185-1_arm64.deb ... Unpacking libdevmapper1.02.1:arm64 (2:1.02.185-1) ... Selecting previously unselected package libjson-c5:arm64. Preparing to unpack .../003-libjson-c5_0.16-1_arm64.deb ... Unpacking libjson-c5:arm64 (0.16-1) ... Selecting previously unselected package libcryptsetup12:arm64. Preparing to unpack .../004-libcryptsetup12_2%3a2.5.0-2_arm64.deb ... Unpacking libcryptsetup12:arm64 (2:2.5.0-2) ... Selecting previously unselected package libfdisk1:arm64. Preparing to unpack .../005-libfdisk1_2.38.1-1_arm64.deb ... 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Unpacking bsdextrautils (2.38.1-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../024-libpipeline1_1.5.6-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.6-2) ... Selecting previously unselected package man-db. Preparing to unpack .../025-man-db_2.10.2-2_arm64.deb ... Unpacking man-db (2.10.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../026-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package m4. Preparing to unpack .../027-m4_1.4.19-1_arm64.deb ... Unpacking m4 (1.4.19-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../028-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../029-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. 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Preparing to unpack .../036-libsasl2-modules-db_2.1.28+dfsg-7_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-7) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../037-libsasl2-2_2.1.28+dfsg-7_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-7) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../038-libldap-2.5-0_2.5.12+dfsg-2+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.12+dfsg-2+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../039-libnghttp2-14_1.48.0-2_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.48.0-2) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../040-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../041-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... 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Unpacking libuv1:arm64 (1.44.2-1) ... Selecting previously unselected package dh-elpa-helper. Preparing to unpack .../048-dh-elpa-helper_2.0.10_all.deb ... Unpacking dh-elpa-helper (2.0.10) ... Selecting previously unselected package emacsen-common. Preparing to unpack .../049-emacsen-common_3.0.4_all.deb ... Unpacking emacsen-common (3.0.4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../050-cmake-data_3.24.1-1_all.deb ... Unpacking cmake-data (3.24.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../051-cmake_3.24.1-1_arm64.deb ... Unpacking cmake (3.24.1-1) ... Selecting previously unselected package gcc-12-x86-64-linux-gnu-base:arm64. Preparing to unpack .../052-gcc-12-x86-64-linux-gnu-base_12.1.0-7cross1_arm64.deb ... Unpacking gcc-12-x86-64-linux-gnu-base:arm64 (12.1.0-7cross1) ... Selecting previously unselected package cpp-12-x86-64-linux-gnu. 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Selecting previously unselected package libc6-dev-amd64-cross. Preparing to unpack .../073-libc6-dev-amd64-cross_2.34-3cross1_all.deb ... Unpacking libc6-dev-amd64-cross (2.34-3cross1) ... Selecting previously unselected package libstdc++-12-dev-amd64-cross. Preparing to unpack .../074-libstdc++-12-dev-amd64-cross_12.1.0-8cross1_all.deb ... Unpacking libstdc++-12-dev-amd64-cross (12.1.0-8cross1) ... Selecting previously unselected package g++-12-x86-64-linux-gnu. Preparing to unpack .../075-g++-12-x86-64-linux-gnu_12.1.0-7cross1_arm64.deb ... Unpacking g++-12-x86-64-linux-gnu (12.1.0-7cross1) ... Selecting previously unselected package g++-x86-64-linux-gnu. Preparing to unpack .../076-g++-x86-64-linux-gnu_4%3a12.1.0-3_arm64.deb ... Unpacking g++-x86-64-linux-gnu (4:12.1.0-3) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../077-libconfig-inifiles-perl_3.000003-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../078-libio-string-perl_1.08-3.1_all.deb ... Unpacking libio-string-perl (1.08-3.1) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../079-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../080-libxml-sax-base-perl_1.09-2_all.deb ... Unpacking libxml-sax-base-perl (1.09-2) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../081-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../082-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1_arm64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... Selecting previously unselected package libxml-simple-perl. 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Selecting previously unselected package libsimbody3.6:amd64. Preparing to unpack .../238-libsimbody3.6_3.6.1+dfsg-7_amd64.deb ... Unpacking libsimbody3.6:amd64 (3.6.1+dfsg-7) ... Selecting previously unselected package libsimbody-dev:amd64. Preparing to unpack .../239-libsimbody-dev_3.6.1+dfsg-7_amd64.deb ... Unpacking libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Selecting previously unselected package libstdc++-12-dev:amd64. Preparing to unpack .../240-libstdc++-12-dev_12.1.0-8_amd64.deb ... Unpacking libstdc++-12-dev:amd64 (12.1.0-8) ... Selecting previously unselected package tao-pegtl-dev. Preparing to unpack .../241-tao-pegtl-dev_3.2.7-1_all.deb ... Unpacking tao-pegtl-dev (3.2.7-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../242-zlib1g-dev_1%3a1.2.11.dfsg-4.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-4.1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:amd64. 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-7) ... Setting up libnghttp2-14:arm64 (1.48.0-2) ... Setting up libmagic1:arm64 (1:5.41-4) ... Setting up linux-libc-dev:amd64 (5.18.16-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-8) ... Setting up m4 (1.4.19-1) ... Setting up file (1:5.41-4) ... Setting up libyaml-perl (1.30-1) ... Setting up libgomp1-amd64-cross (12.1.0-8cross1) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libpthread-stubs0-dev:arm64 (0.4-1) ... Setting up gcc-12-base:amd64 (12.1.0-8) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-7) ... Setting up libitm1-amd64-cross (12.1.0-8cross1) ... Setting up libxml-sax-base-perl (1.09-2) ... Setting up libio-string-perl (1.08-3.1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.18+nmu2) ... Setting up libuv1:arm64 (1.44.2-1) ... Setting up libatomic1-amd64-cross (12.1.0-8cross1) ... Setting up emacsen-common (3.0.4) ... Setting up libx11-data (2:1.8.1-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up dh-elpa-helper (2.0.10) ... Setting up libncurses6:arm64 (6.3+20220423-2) ... Setting up libquadmath0-amd64-cross (12.1.0-8cross1) ... Setting up autopoint (0.21-8) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... Setting up libc6-amd64-cross (2.34-3cross1) ... Setting up libncursesw6:arm64 (6.3+20220423-2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-7) ... Setting up autoconf (2.71-2) ... Setting up libfdisk1:arm64 (2.38.1-1) ... Setting up libmd0:arm64 (1.0.4-2) ... Setting up sensible-utils (0.0.17) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-3) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.24.1-1) ... Setting up libgcc-s1-amd64-cross (12.1.0-8cross1) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up libbsd0:arm64 (0.11.6-1) ... Setting up libdrm-common (2.4.112-3) ... Setting up libelf1:arm64 (0.187-1) ... Setting up libjson-c5:arm64 (0.16-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1+b1) ... Setting up liblocale-gettext-perl (1.07-4+b2) ... Setting up libprocps8:arm64 (2:3.3.17-7+b1) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libkmod2:arm64 (30+20220630-3) ... Setting up gcc-12-x86-64-linux-gnu-base:arm64 (12.1.0-7cross1) ... Setting up binutils-x86-64-linux-gnu (2.38.90.20220713-2) ... Setting up cpp-12-x86-64-linux-gnu (12.1.0-7cross1) ... Setting up libstdc++6-amd64-cross (12.1.0-8cross1) ... Setting up cpp-x86-64-linux-gnu (4:12.1.0-3) ... 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 (1.13.0-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-8) ... Setting up libtool (2.4.7-4) ... Setting up libarchive13:arm64 (3.6.0-1) ... Setting up libasan8-amd64-cross (12.1.0-8cross1) ... Setting up liblsan0-amd64-cross (12.1.0-8cross1) ... Setting up libc6-dev-amd64-cross (2.34-3cross1) ... Setting up libtsan2-amd64-cross (12.1.0-8cross1) ... Setting up libldap-2.5-0:arm64 (2.5.12+dfsg-2+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dh-autoreconf (20) ... Setting up libsystemd-shared:arm64 (251.4-1) ... Setting up libubsan1-amd64-cross (12.1.0-8cross1) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-8) ... Setting up procps (2:3.3.17-7+b1) ... Setting up libcurl4:arm64 (7.84.0-2) ... Setting up libx11-6:arm64 (2:1.8.1-2) ... Setting up libgcc-12-dev-amd64-cross (12.1.0-8cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libstdc++-12-dev-amd64-cross (12.1.0-8cross1) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up cmake (3.24.1-1) ... Setting up gcc-12-x86-64-linux-gnu (12.1.0-7cross1) ... Setting up gcc-x86-64-linux-gnu (4:12.1.0-3) ... Setting up libxml-simple-perl (2.25-1) ... Setting up g++-12-x86-64-linux-gnu (12.1.0-7cross1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-x86-64-linux-gnu (4:12.1.0-3) ... Setting up libdebian-dpkgcross-perl (2.6.18+nmu2) ... Setting up dpkg-cross (2.6.18+nmu2) ... Setting up crossbuild-essential-amd64 (12.9) ... Setting up libdevmapper1.02.1:arm64 (2:1.02.185-1) ... Setting up dmsetup (2:1.02.185-1) ... Setting up libcryptsetup12:arm64 (2:2.5.0-2) ... Setting up systemd (251.4-1) ... Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /lib/systemd/system/getty@.service. Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /lib/systemd/system/remote-fs.target. Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service → /lib/systemd/system/systemd-pstore.service. Initializing machine ID from random generator. Setting up man-db (2.10.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libgcc-s1:amd64 (12.1.0-8) ... Setting up libc6:amd64 (2.34-4) ... Setting up libffi8:amd64 (3.4.2-4) ... Setting up libdrm2:amd64 (2.4.112-3) ... Setting up libmd0:amd64 (1.0.4-2) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libasan8:amd64 (12.1.0-8) ... Setting up libtsan2:amd64 (12.1.0-8) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up libstdc++6:amd64 (12.1.0-8) ... Setting up liblsan0:amd64 (12.1.0-8) ... Setting up libitm1:amd64 (12.1.0-8) ... Setting up libtinfo6:amd64 (6.3+20220423-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.112-3) ... Setting up libwayland-client0:amd64 (1.21.0-1) ... Setting up libexpat1:amd64 (2.4.8-1) ... Setting up libicu71:amd64 (71.1-3) ... Setting up libwayland-server0:amd64 (1.21.0-1) ... Setting up libzstd1:amd64 (1.5.2+dfsg-1) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.6.3-1) ... Setting up libdrm-nouveau2:amd64 (2.4.112-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up liblzma5:amd64 (5.2.5-2.1) ... Setting up libgbm1:amd64 (22.2.0~rc2-1) ... Setting up libmmdb2-0:amd64 (2.0.22-1) ... Setting up libdrm-radeon1:amd64 (2.4.112-3) ... Setting up libglvnd0:amd64 (1.4.0-1) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up libssl3:amd64 (3.0.5-2) ... Setting up debhelper (13.9) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-4.1) ... Setting up libcrypt1:amd64 (1:4.4.28-2) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libcom-err2:amd64 (1.46.5-2) ... Setting up libgomp1:amd64 (12.1.0-8) ... Setting up libopengl0:amd64 (1.4.0-1) ... Setting up libkrb5support0:amd64 (1.20-1) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libz3-4:amd64 (4.8.12-1+b1) ... Setting up libblas3:amd64 (3.10.1-2) ... 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 libgles2:amd64 (1.4.0-1) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up libgles1:amd64 (1.4.0-1) ... Setting up libquadmath0:amd64 (12.1.0-8) ... Setting up libatomic1:amd64 (12.1.0-8) ... Setting up libuuid1:amd64 (2.38.1-1) ... Setting up libmmdb2-dev:amd64 (2.0.22-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libk5crypto3:amd64 (1.20-1) ... Setting up libglapi-mesa:amd64 (22.2.0~rc2-1) ... Setting up libgfortran5:amd64 (12.1.0-8) ... Setting up libubsan1:amd64 (12.1.0-8) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libcrypt-dev:amd64 (1:4.4.28-2) ... Setting up libx11-6:amd64 (2:1.8.1-2) ... Setting up libkrb5-3:amd64 (1.20-1) ... Setting up libglu1-mesa:amd64 (9.0.2-1) ... Setting up libopengl-dev:amd64 (1.4.0-1) ... Setting up libelf1:amd64 (0.187-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1+b1) ... Setting up libblas-dev:amd64 (3.10.1-2) ... 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 libxcb-dri3-0:amd64 (1.15-1) ... Setting up libx11-xcb1:amd64 (2:1.8.1-2) ... Setting up liblapack3:amd64 (3.10.1-2) ... 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 libxext6:amd64 (2:1.3.4-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libegl-mesa0:amd64 (22.2.0~rc2-1) ... Setting up libxfixes3:amd64 (1:6.0.0-1) ... Setting up libgcc-12-dev:amd64 (12.1.0-8) ... Setting up liblapack-dev:amd64 (3.10.1-2) ... 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 (1.20-1) ... Setting up libxt6:amd64 (1:1.2.1-1) ... Setting up libllvm14:amd64 (1:14.0.6-2) ... Setting up libegl1:amd64 (1.4.0-1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up libxi6:amd64 (2:1.8-1) ... Setting up libgl1-mesa-dri:amd64 (22.2.0~rc2-1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libglx-mesa0:amd64 (22.2.0~rc2-1) ... Setting up libglx0:amd64 (1.4.0-1) ... Setting up libgl1:amd64 (1.4.0-1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.34-4) ... Setting up freeglut3:amd64 (2.8.1-6) ... Setting up libstdc++-12-dev:amd64 (12.1.0-8) ... Setting up libsimbody3.6:amd64 (3.6.1+dfsg-7) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-4.1) ... Processing triggers for sgml-base (1.30) ... Setting up x11proto-dev (2022.1-1) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up libxau-dev:arm64 (1:1.0.9-1) ... Setting up libice-dev:amd64 (2:1.0.10-1) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Processing triggers for libc-bin (2.34-4) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libxcb1-dev:arm64 (1.15-1) ... Setting up libx11-dev:amd64 (2:1.8.1-2) ... Setting up libx11-dev:arm64 (2:1.8.1-2) ... Setting up libxfixes-dev:amd64 (1:6.0.0-1) ... Setting up libxt-dev:amd64 (1:1.2.1-1) ... Setting up libxext-dev:amd64 (2:1.3.4-1) ... Setting up libglx-dev:amd64 (1.4.0-1) ... Setting up libxi-dev:amd64 (2:1.8-1) ... Setting up libgl-dev:amd64 (1.4.0-1) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libegl-dev:amd64 (1.4.0-1) ... Setting up libxmu-dev:amd64 (2:1.1.3-3) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1) ... Setting up libgles-dev:amd64 (1.4.0-1) ... Setting up libglvnd-dev:amd64 (1.4.0-1) ... Setting up libgl1-mesa-dev:amd64 (22.2.0~rc2-1) ... Setting up freeglut3-dev:amd64 (2.8.1-6) ... Setting up libsimbody-dev:amd64 (3.6.1+dfsg-7) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64) Toolchain package versions: binutils_2.38.90.20220713-2 dpkg-dev_1.21.9 g++-12_12.1.0-8 gcc-12_12.1.0-8 libc6-dev_2.34-4 libstdc++-12-dev_12.1.0-8 libstdc++-12-dev-amd64-cross_12.1.0-8cross1 libstdc++6_12.1.0-8 libstdc++6-amd64-cross_12.1.0-8cross1 linux-libc-dev_5.18.16-1 Package versions: adduser_3.127 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.2 base-passwd_3.6.0 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passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7+b1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.4-1 sysvinit-utils_3.04-1 tao-pegtl-dev_3.2.7-1 tar_1.34+dfsg-1 tzdata_2022c-1 ucf_3.0043 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 x11-common_1:7.7+23 x11proto-dev_2022.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: molmodel Binary: libsimtkmolmodel-dev, libsimtkmolmodel3.0 Architecture: any Version: 3.0.113.gd05a5b6-2 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/molmodel Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/debichem-team/molmodel Vcs-Git: https://salsa.debian.org/debichem-team/molmodel.git Build-Depends: cmake, debhelper-compat (= 13), gemmi-dev, libmmdb2-dev, libsimbody-dev, tao-pegtl-dev, zlib1g-dev Package-List: libsimtkmolmodel-dev deb libdevel optional arch=any libsimtkmolmodel3.0 deb libs optional arch=any Checksums-Sha1: 97ca25b063e7fd8b75e380729c0eac0a9a776231 8554616 molmodel_3.0.113.gd05a5b6.orig.tar.xz 141b0a3c1b9f07c7b840a1bbb297043414e0b861 3116 molmodel_3.0.113.gd05a5b6-2.debian.tar.xz Checksums-Sha256: d29c02a072deb95075440f4b5da94a72962c449a33a129164cdd97dd3622ba48 8554616 molmodel_3.0.113.gd05a5b6.orig.tar.xz 3c771120f29237da31e12f31692e0df5c40162c9d8520e506be737298ce40e22 3116 molmodel_3.0.113.gd05a5b6-2.debian.tar.xz Files: eb265197ce92bda2e501a48136ab3822 8554616 molmodel_3.0.113.gd05a5b6.orig.tar.xz 0bf6abd7b6cecbdf8a8e4610126c3a2c 3116 molmodel_3.0.113.gd05a5b6-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmKUwgYSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKH5jsP/0ayZX+skS/8ygmmPiXwBBdMC3ETIFws k737Y0XkmTlpRqWyLrcGW5/nyORm37ngo8I7X0ufEYWXZ8lFQLZeFbCSMnlIgO6Z k6zpl/50WXe37Gg6qd1vygLYAjFOjVlg0O5QDQqX5BH6Ht1UGGsMdF32obtn6hl8 dv6aaBO5vq2YPHlodhWCUXnZw190jXFtJz4VVnpfOYGytqzlqv+EKfHBAT4Bx0vc Dxs3hLLDNORsxAkSnwUZI2M1JQvnrMqW+n8Ky7Y25ztH04o9A9MQBm70/Bbkcs5O jDyevdhyIukE3XFObTtSFWbc/l25P1t7sShaTEd9ZWHRn2/za3Vj1EKCMTPtA8MP KVVi4nj7bqwktV3+HoLo+WxTNtnOKxeBK8CMY7se2RoCs6VrQnHPCnGSioQlSBN2 CfBC8W654oXLXQGRDa9ODLwxDH1bWevLTLhqtBhpYq3NvT9IaAw09pTz0CjO8KbZ E2hBbdKq9A0uYiqL1jETw0ToiACtyJSo30TxeKLJtjZvKrYDo4MgbsqOYswKM5pm w64LdT235MP3tkiiCeS4reSue6ouPJ4p5Le/WcBKedIiar2DvvMosjDoFb/C5I6U mLSFbfy+hqAKQEmju4M9+sIrNRfduk2Ghtq3CF0Q2HhsAGJhEBXG2OXpE2aX5qvk lZhhbSBy/EUG =3hO3 -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.nHMG_69q/trustedkeys.kbx': General error gpgv: Signature made Mon May 30 13:09:26 2022 UTC gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./molmodel_3.0.113.gd05a5b6-2.dsc dpkg-source: info: extracting molmodel in /<> dpkg-source: info: unpacking molmodel_3.0.113.gd05a5b6.orig.tar.xz dpkg-source: info: unpacking molmodel_3.0.113.gd05a5b6-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ ulimit -c --------- 0 I: Finished running 'ulimit -c'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmutg PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=crossqa-sid SCHROOT_CHROOT_NAME=crossqa-sid SCHROOT_COMMAND=env SCHROOT_GID=1002 SCHROOT_GROUP=helmutg SCHROOT_SESSION_ID=crossqa-sid-a55b5efb-04c7-4e4d-9f5c-104f974b2e29 SCHROOT_UID=1002 SCHROOT_USER=helmutg SHELL=/bin/sh USER=helmutg dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.0.113.gd05a5b6-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- -DBUILD_EXAMPLES=OFF 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_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=x86_64 -DCMAKE_C_COMPILER=x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/x86_64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_EXAMPLES=OFF .. CMake Deprecation Warning at CMakeLists.txt:31 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.1.0 -- The CXX compiler identification is GNU 12.1.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/x86_64-linux-gnu-gcc - 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/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Could NOT find OpenMM (missing: OpenMM_INCLUDE_DIR OpenMM_LIBRARIES) CMake Deprecation Warning at cmake_modules/FindSimbody.cmake:74 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. Call Stack (most recent call first): CMakeLists.txt:169 (find_package) -- Could not find 'svnversion' executable; 'about' will be wrong. (Cygwin provides one on Windows.) -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- 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 PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 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 sharedTarget/CMakeFiles/SimTKmolmodel.dir/build.make sharedTarget/CMakeFiles/SimTKmolmodel.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" /<> /<>/sharedTarget /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/sharedTarget /<>/obj-x86_64-linux-gnu/sharedTarget/CMakeFiles/SimTKmolmodel.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f sharedTarget/CMakeFiles/SimTKmolmodel.dir/build.make sharedTarget/CMakeFiles/SimTKmolmodel.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o -c /<>/src/About.cpp [ 1%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o -c /<>/src/AtomSubsystem.cpp In file included from /<>/src/AtomSubsystem.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/./include/molmodel/internal/AtomSubsystem.h:4: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 2%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o -c /<>/src/Biotype.cpp [ 3%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o -c /<>/src/BondGeometry.cpp [ 4%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o -c /<>/src/Compound.cpp In file included from /<>/src/CompoundAtom.h:36, from /<>/src/CompoundRep.h:42, from /<>/src/Compound.cpp:45: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/src/Compound.cpp:32: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o -c /<>/src/CompoundSystem.cpp In file included from /<>/src/CompoundAtom.h:36, from /<>/src/CompoundRep.h:42, from /<>/src/CompoundSystem.cpp:3: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/./include/molmodel/internal/CompoundSystem.h:4, from /<>/src/CompoundSystem.cpp:1: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o -c /<>/src/DuMMForceFieldSubsystem.cpp In file included from /<>/src/gbsa/ObcParameters.h:28, from /<>/src/DuMMForceFieldSubsystemRep.h:50, from /<>/src/DuMMForceFieldSubsystem.cpp:43: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/./include/molmodel/internal/common.h:40, from /<>/src/DuMMForceFieldSubsystem.cpp:40: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 6%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o -c /<>/src/DuMMForceFieldSubsystemRep.cpp In file included from /<>/src/gbsa/ObcParameters.h:28, from /<>/src/DuMMForceFieldSubsystemRep.h:50, from /<>/src/DuMMForceFieldSubsystemRep.cpp:40: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/./include/molmodel/internal/common.h:40, from /<>/src/DuMMForceFieldSubsystemRep.cpp:38: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o -c /<>/src/Element.cpp [ 8%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o -c /<>/src/MolecularMechanicsSystem.cpp [ 9%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o -c /<>/src/PDBReader.cpp [ 10%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o -c /<>/src/Pdb.cpp [ 10%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o -c /<>/src/PeriodicVmdReporter.cpp [ 11%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Representation.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Representation.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/Representation.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/Representation.cpp.o -c /<>/src/Representation.cpp [ 12%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o -c /<>/src/RiboseMobilizer.cpp [ 13%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o -c /<>/src/TinkerAmber99.cpp [ 14%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o -c /<>/src/VanderWallSphere.cpp [ 15%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o -c /<>/src/VelocityRescalingThermostat.cpp [ 15%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o -c /<>/src/VmdConnection.cpp [ 16%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o -c /<>/src/gbsa/CpuImplicitSolvent.cpp In file included from /<>/src/gbsa/CpuImplicitSolvent.cpp:25: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuObc.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuObc.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuObc.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuObc.cpp.o -c /<>/src/gbsa/CpuObc.cpp In file included from /<>/src/gbsa/CpuObc.cpp:26: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ImplicitSolventParameters.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ImplicitSolventParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ImplicitSolventParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ImplicitSolventParameters.cpp.o -c /<>/src/gbsa/ImplicitSolventParameters.cpp In file included from /<>/src/gbsa/ImplicitSolventParameters.cpp:25: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ObcParameters.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ObcParameters.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ObcParameters.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ObcParameters.cpp.o -c /<>/src/gbsa/ObcParameters.cpp In file included from /<>/src/gbsa/ObcParameters.h:28, from /<>/src/gbsa/ObcParameters.cpp:26: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMCommon.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMCommon.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMCommon.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMCommon.cpp.o -c /<>/src/gbsa/SimTKOpenMMCommon.cpp In file included from /<>/src/gbsa/SimTKOpenMMCommon.cpp:25: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMLog.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMLog.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMLog.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMLog.cpp.o -c /<>/src/gbsa/SimTKOpenMMLog.cpp In file included from /<>/src/gbsa/SimTKOpenMMLog.h:28, from /<>/src/gbsa/SimTKOpenMMLog.cpp:25: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMUtilities.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMUtilities.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMUtilities.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMUtilities.cpp.o -c /<>/src/gbsa/SimTKOpenMMUtilities.cpp In file included from /<>/src/gbsa/SimTKOpenMMUtilities.h:30, from /<>/src/gbsa/SimTKOpenMMUtilities.cpp:27: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/SimTKOpenMMCommon.h:28: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o -c /<>/src/gbsa/cpuObcInterface.cpp In file included from /<>/src/gbsa/SimTKOpenMMLog.h:28, from /<>/src/gbsa/cpuObcInterface.cpp:27: /<>/src/gbsa/SimTKOpenMMCommon.h:163:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 163 | class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > { | ^~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/string:48, from /usr/x86_64-linux-gnu/include/c++/12/bits/locale_classes.h:40, from /usr/x86_64-linux-gnu/include/c++/12/bits/ios_base.h:41, from /usr/x86_64-linux-gnu/include/c++/12/ios:42, from /usr/x86_64-linux-gnu/include/c++/12/istream:38, from /usr/x86_64-linux-gnu/include/c++/12/sstream:38, from /usr/x86_64-linux-gnu/include/c++/12/complex:45, from /usr/include/simbody/SimTKcommon/internal/common.h:257, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /<>/src/gbsa/cpuObcInterface.h:34, from /<>/src/gbsa/cpuObcInterface.cpp:25: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /<>/src/gbsa/SimTKOpenMMCommon.h:172:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 172 | class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > { | ^~~~~~~~~~~~~~~ /usr/x86_64-linux-gnu/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 23%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o -c /<>/src/imd.cpp [ 24%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.cpp.o cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -fPIC -MD -MT sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.cpp.o -MF CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.cpp.o.d -o CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.cpp.o -c /<>/src/vmdsock.cpp [ 24%] Linking CXX shared library ../libSimTKmolmodel.so cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimTKmolmodel.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -fPIC -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fvisibility=hidden -Wl,-z,relro -shared -Wl,-soname,libSimTKmolmodel.so.3.0 -o ../libSimTKmolmodel.so.3.0 CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/Representation.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuObc.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ImplicitSolventParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/ObcParameters.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMCommon.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMLog.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/SimTKOpenMMUtilities.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.cpp.o /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.6 -lz /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.6 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm cd /<>/obj-x86_64-linux-gnu/sharedTarget && /usr/bin/cmake -E cmake_symlink_library ../libSimTKmolmodel.so.3.0 ../libSimTKmolmodel.so.3.0 ../libSimTKmolmodel.so make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 24%] Built target SimTKmolmodel make -f tests/CMakeFiles/TestAtomTargetLocations.dir/build.make tests/CMakeFiles/TestAtomTargetLocations.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestAtomTargetLocations.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestAtomTargetLocations.dir/build.make tests/CMakeFiles/TestAtomTargetLocations.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 25%] Building CXX object tests/CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -MF CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o.d -o CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -c /<>/tests/TestAtomTargetLocations.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestAtomTargetLocations.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Linking CXX executable ../TestAtomTargetLocations cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestAtomTargetLocations.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -o ../TestAtomTargetLocations -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 26%] Built target TestAtomTargetLocations make -f tests/CMakeFiles/TestBiopolymer.dir/build.make tests/CMakeFiles/TestBiopolymer.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestBiopolymer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestBiopolymer.dir/build.make tests/CMakeFiles/TestBiopolymer.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 27%] Building CXX object tests/CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -MF CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o.d -o CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -c /<>/tests/TestBiopolymer.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestBiopolymer.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Linking CXX executable ../TestBiopolymer cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiopolymer.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -o ../TestBiopolymer -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 28%] Built target TestBiopolymer make -f tests/CMakeFiles/TestBiotypeSelfCode.dir/build.make tests/CMakeFiles/TestBiotypeSelfCode.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestBiotypeSelfCode.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestBiotypeSelfCode.dir/build.make tests/CMakeFiles/TestBiotypeSelfCode.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 28%] Building CXX object tests/CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -MF CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o.d -o CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -c /<>/tests/TestBiotypeSelfCode.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestBiotypeSelfCode.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Linking CXX executable ../TestBiotypeSelfCode cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiotypeSelfCode.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -o ../TestBiotypeSelfCode -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 29%] Built target TestBiotypeSelfCode make -f tests/CMakeFiles/TestBodyIds.dir/build.make tests/CMakeFiles/TestBodyIds.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestBodyIds.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestBodyIds.dir/build.make tests/CMakeFiles/TestBodyIds.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 30%] Building CXX object tests/CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -MF CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o.d -o CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -c /<>/tests/TestBodyIds.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestBodyIds.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Linking CXX executable ../TestBodyIds cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBodyIds.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -o ../TestBodyIds -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 31%] Built target TestBodyIds make -f tests/CMakeFiles/TestCompoundTransforms.dir/build.make tests/CMakeFiles/TestCompoundTransforms.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestCompoundTransforms.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestCompoundTransforms.dir/build.make tests/CMakeFiles/TestCompoundTransforms.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 32%] Building CXX object tests/CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -MF CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o.d -o CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -c /<>/tests/TestCompoundTransforms.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestCompoundTransforms.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Linking CXX executable ../TestCompoundTransforms cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestCompoundTransforms.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -o ../TestCompoundTransforms -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 33%] Built target TestCompoundTransforms make -f tests/CMakeFiles/TestDihedrals2.dir/build.make tests/CMakeFiles/TestDihedrals2.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestDihedrals2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestDihedrals2.dir/build.make tests/CMakeFiles/TestDihedrals2.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 33%] Building CXX object tests/CMakeFiles/TestDihedrals2.dir/TestDihedrals2.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestDihedrals2.dir/TestDihedrals2.cpp.o -MF CMakeFiles/TestDihedrals2.dir/TestDihedrals2.cpp.o.d -o CMakeFiles/TestDihedrals2.dir/TestDihedrals2.cpp.o -c /<>/tests/TestDihedrals2.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestDihedrals2.cpp:2: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Linking CXX executable ../TestDihedrals2 cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestDihedrals2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestDihedrals2.dir/TestDihedrals2.cpp.o -o ../TestDihedrals2 -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 34%] Built target TestDihedrals2 make -f tests/CMakeFiles/TestDuMMForces.dir/build.make tests/CMakeFiles/TestDuMMForces.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestDuMMForces.dir/build.make tests/CMakeFiles/TestDuMMForces.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 35%] Building CXX object tests/CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -MF CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o.d -o CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -c /<>/tests/TestDuMMForces.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestDuMMForces.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Linking CXX executable ../TestDuMMForces cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestDuMMForces.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -o ../TestDuMMForces -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 36%] Built target TestDuMMForces make -f tests/CMakeFiles/TestEthane.dir/build.make tests/CMakeFiles/TestEthane.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestEthane.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestEthane.dir/build.make tests/CMakeFiles/TestEthane.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 37%] Building CXX object tests/CMakeFiles/TestEthane.dir/TestEthane.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestEthane.dir/TestEthane.cpp.o -MF CMakeFiles/TestEthane.dir/TestEthane.cpp.o.d -o CMakeFiles/TestEthane.dir/TestEthane.cpp.o -c /<>/tests/TestEthane.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestEthane.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Linking CXX executable ../TestEthane cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthane.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestEthane.dir/TestEthane.cpp.o -o ../TestEthane -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 37%] Built target TestEthane make -f tests/CMakeFiles/TestFitMagnesiums.dir/build.make tests/CMakeFiles/TestFitMagnesiums.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestFitMagnesiums.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestFitMagnesiums.dir/build.make tests/CMakeFiles/TestFitMagnesiums.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 38%] Building CXX object tests/CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -MF CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o.d -o CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -c /<>/tests/TestFitMagnesiums.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestFitMagnesiums.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Linking CXX executable ../TestFitMagnesiums cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestFitMagnesiums.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -o ../TestFitMagnesiums -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 39%] Built target TestFitMagnesiums make -f tests/CMakeFiles/TestForeignBodyIds.dir/build.make tests/CMakeFiles/TestForeignBodyIds.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestForeignBodyIds.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestForeignBodyIds.dir/build.make tests/CMakeFiles/TestForeignBodyIds.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 40%] Building CXX object tests/CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -MF CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o.d -o CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -c /<>/tests/TestForeignBodyIds.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestForeignBodyIds.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Linking CXX executable ../TestForeignBodyIds cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestForeignBodyIds.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -o ../TestForeignBodyIds -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 40%] Built target TestForeignBodyIds make -f tests/CMakeFiles/TestGbsa.dir/build.make tests/CMakeFiles/TestGbsa.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestGbsa.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestGbsa.dir/build.make tests/CMakeFiles/TestGbsa.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 41%] Building CXX object tests/CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -MF CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o.d -o CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -c /<>/tests/TestGbsa.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestGbsa.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Linking CXX executable ../TestGbsa cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGbsa.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -o ../TestGbsa -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 42%] Built target TestGbsa make -f tests/CMakeFiles/TestGetAtomName.dir/build.make tests/CMakeFiles/TestGetAtomName.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestGetAtomName.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestGetAtomName.dir/build.make tests/CMakeFiles/TestGetAtomName.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 43%] Building CXX object tests/CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -MF CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o.d -o CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -c /<>/tests/TestGetAtomName.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestGetAtomName.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Linking CXX executable ../TestGetAtomName cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGetAtomName.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -o ../TestGetAtomName -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 44%] Built target TestGetAtomName make -f tests/CMakeFiles/TestLoadPdb.dir/build.make tests/CMakeFiles/TestLoadPdb.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestLoadPdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestLoadPdb.dir/build.make tests/CMakeFiles/TestLoadPdb.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 45%] Building CXX object tests/CMakeFiles/TestLoadPdb.dir/TestLoadPdb.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestLoadPdb.dir/TestLoadPdb.cpp.o -MF CMakeFiles/TestLoadPdb.dir/TestLoadPdb.cpp.o.d -o CMakeFiles/TestLoadPdb.dir/TestLoadPdb.cpp.o -c /<>/tests/TestLoadPdb.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestLoadPdb.cpp:4: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/./include/molmodel/internal/Compound.h:36, from /<>/tests/TestLoadPdb.cpp:2: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Linking CXX executable ../TestLoadPdb cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoadPdb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestLoadPdb.dir/TestLoadPdb.cpp.o -o ../TestLoadPdb -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 45%] Built target TestLoadPdb make -f tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build.make tests/CMakeFiles/TestLoadVariantRnaAtomNames.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build.make tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 46%] Building CXX object tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -MF CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o.d -o CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -c /<>/tests/TestLoadVariantRnaAtomNames.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestLoadVariantRnaAtomNames.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Linking CXX executable ../TestLoadVariantRnaAtomNames cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoadVariantRnaAtomNames.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -o ../TestLoadVariantRnaAtomNames -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 47%] Built target TestLoadVariantRnaAtomNames make -f tests/CMakeFiles/TestLoneAtomCoordinates.dir/build.make tests/CMakeFiles/TestLoneAtomCoordinates.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestLoneAtomCoordinates.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestLoneAtomCoordinates.dir/build.make tests/CMakeFiles/TestLoneAtomCoordinates.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 48%] Building CXX object tests/CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -MF CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o.d -o CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -c /<>/tests/TestLoneAtomCoordinates.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestLoneAtomCoordinates.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Linking CXX executable ../TestLoneAtomCoordinates cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoneAtomCoordinates.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -o ../TestLoneAtomCoordinates -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 49%] Built target TestLoneAtomCoordinates make -f tests/CMakeFiles/TestMethaneCartesian.dir/build.make tests/CMakeFiles/TestMethaneCartesian.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestMethaneCartesian.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestMethaneCartesian.dir/build.make tests/CMakeFiles/TestMethaneCartesian.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 50%] Building CXX object tests/CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -MF CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o.d -o CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -c /<>/tests/TestMethaneCartesian.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestMethaneCartesian.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Linking CXX executable ../TestMethaneCartesian cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethaneCartesian.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -o ../TestMethaneCartesian -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 51%] Built target TestMethaneCartesian make -f tests/CMakeFiles/TestMethanol.dir/build.make tests/CMakeFiles/TestMethanol.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestMethanol.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestMethanol.dir/build.make tests/CMakeFiles/TestMethanol.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 52%] Building CXX object tests/CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -MF CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o.d -o CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -c /<>/tests/TestMethanol.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestMethanol.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Linking CXX executable ../TestMethanol cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethanol.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -o ../TestMethanol -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 53%] Built target TestMethanol make -f tests/CMakeFiles/TestMgSolvationEnergy.dir/build.make tests/CMakeFiles/TestMgSolvationEnergy.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestMgSolvationEnergy.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestMgSolvationEnergy.dir/build.make tests/CMakeFiles/TestMgSolvationEnergy.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 53%] Building CXX object tests/CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -MF CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o.d -o CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -c /<>/tests/TestMgSolvationEnergy.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestMgSolvationEnergy.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Linking CXX executable ../TestMgSolvationEnergy cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMgSolvationEnergy.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -o ../TestMgSolvationEnergy -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 54%] Built target TestMgSolvationEnergy make -f tests/CMakeFiles/TestNoseHooverThermostat.dir/build.make tests/CMakeFiles/TestNoseHooverThermostat.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestNoseHooverThermostat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestNoseHooverThermostat.dir/build.make tests/CMakeFiles/TestNoseHooverThermostat.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 55%] Building CXX object tests/CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -MF CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o.d -o CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -c /<>/tests/TestNoseHooverThermostat.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestNoseHooverThermostat.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Linking CXX executable ../TestNoseHooverThermostat cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNoseHooverThermostat.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -o ../TestNoseHooverThermostat -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 56%] Built target TestNoseHooverThermostat make -f tests/CMakeFiles/TestNucleotide2.dir/build.make tests/CMakeFiles/TestNucleotide2.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestNucleotide2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestNucleotide2.dir/build.make tests/CMakeFiles/TestNucleotide2.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 57%] Building CXX object tests/CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -MF CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o.d -o CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -c /<>/tests/TestNucleotide2.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestNucleotide2.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 57%] Linking CXX executable ../TestNucleotide2 cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNucleotide2.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -o ../TestNucleotide2 -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 57%] Built target TestNucleotide2 make -f tests/CMakeFiles/TestOxygenMolecule.dir/build.make tests/CMakeFiles/TestOxygenMolecule.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestOxygenMolecule.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestOxygenMolecule.dir/build.make tests/CMakeFiles/TestOxygenMolecule.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 58%] Building CXX object tests/CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -MF CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o.d -o CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -c /<>/tests/TestOxygenMolecule.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestOxygenMolecule.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 59%] Linking CXX executable ../TestOxygenMolecule cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestOxygenMolecule.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -o ../TestOxygenMolecule -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 59%] Built target TestOxygenMolecule make -f tests/CMakeFiles/TestPartitioner.dir/build.make tests/CMakeFiles/TestPartitioner.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestPartitioner.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestPartitioner.dir/build.make tests/CMakeFiles/TestPartitioner.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 60%] Building CXX object tests/CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -MF CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o.d -o CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -c /<>/tests/TestPartitioner.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestPartitioner.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Linking CXX executable ../TestPartitioner cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitioner.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -o ../TestPartitioner -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 61%] Built target TestPartitioner make -f tests/CMakeFiles/TestPartitionerDihedrals.dir/build.make tests/CMakeFiles/TestPartitionerDihedrals.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestPartitionerDihedrals.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestPartitionerDihedrals.dir/build.make tests/CMakeFiles/TestPartitionerDihedrals.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 62%] Building CXX object tests/CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -MF CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o.d -o CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -c /<>/tests/TestPartitionerDihedrals.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestPartitionerDihedrals.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 62%] Linking CXX executable ../TestPartitionerDihedrals cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitionerDihedrals.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -o ../TestPartitionerDihedrals -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 62%] Built target TestPartitionerDihedrals make -f tests/CMakeFiles/TestPdb.dir/build.make tests/CMakeFiles/TestPdb.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestPdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestPdb.dir/build.make tests/CMakeFiles/TestPdb.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 63%] Building CXX object tests/CMakeFiles/TestPdb.dir/TestPdb.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestPdb.dir/TestPdb.cpp.o -MF CMakeFiles/TestPdb.dir/TestPdb.cpp.o.d -o CMakeFiles/TestPdb.dir/TestPdb.cpp.o -c /<>/tests/TestPdb.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestPdb.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 64%] Linking CXX executable ../TestPdb cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPdb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestPdb.dir/TestPdb.cpp.o -o ../TestPdb -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 64%] Built target TestPdb make -f tests/CMakeFiles/TestPositiveControl.dir/build.make tests/CMakeFiles/TestPositiveControl.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestPositiveControl.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestPositiveControl.dir/build.make tests/CMakeFiles/TestPositiveControl.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 65%] Building CXX object tests/CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -MF CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o.d -o CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -c /<>/tests/TestPositiveControl.cpp [ 66%] Linking CXX executable ../TestPositiveControl cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPositiveControl.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -o ../TestPositiveControl -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 66%] Built target TestPositiveControl make -f tests/CMakeFiles/TestProtein.dir/build.make tests/CMakeFiles/TestProtein.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestProtein.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestProtein.dir/build.make tests/CMakeFiles/TestProtein.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 66%] Building CXX object tests/CMakeFiles/TestProtein.dir/TestProtein.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestProtein.dir/TestProtein.cpp.o -MF CMakeFiles/TestProtein.dir/TestProtein.cpp.o.d -o CMakeFiles/TestProtein.dir/TestProtein.cpp.o -c /<>/tests/TestProtein.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestProtein.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Linking CXX executable ../TestProtein cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProtein.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestProtein.dir/TestProtein.cpp.o -o ../TestProtein -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 67%] Built target TestProtein make -f tests/CMakeFiles/TestProteinDihedrals.dir/build.make tests/CMakeFiles/TestProteinDihedrals.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestProteinDihedrals.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestProteinDihedrals.dir/build.make tests/CMakeFiles/TestProteinDihedrals.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 68%] Building CXX object tests/CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -MF CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o.d -o CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -c /<>/tests/TestProteinDihedrals.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestProteinDihedrals.cpp:2: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Linking CXX executable ../TestProteinDihedrals cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProteinDihedrals.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -o ../TestProteinDihedrals -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 69%] Built target TestProteinDihedrals make -f tests/CMakeFiles/TestRiboseMobilizer.dir/build.make tests/CMakeFiles/TestRiboseMobilizer.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestRiboseMobilizer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestRiboseMobilizer.dir/build.make tests/CMakeFiles/TestRiboseMobilizer.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 70%] Building CXX object tests/CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -MF CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o.d -o CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -c /<>/tests/TestRiboseMobilizer.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestRiboseMobilizer.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 71%] Linking CXX executable ../TestRiboseMobilizer cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRiboseMobilizer.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -o ../TestRiboseMobilizer -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 71%] Built target TestRiboseMobilizer make -f tests/CMakeFiles/TestRna.dir/build.make tests/CMakeFiles/TestRna.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestRna.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestRna.dir/build.make tests/CMakeFiles/TestRna.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 71%] Building CXX object tests/CMakeFiles/TestRna.dir/TestRna.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestRna.dir/TestRna.cpp.o -MF CMakeFiles/TestRna.dir/TestRna.cpp.o.d -o CMakeFiles/TestRna.dir/TestRna.cpp.o -c /<>/tests/TestRna.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestRna.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Linking CXX executable ../TestRna cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRna.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestRna.dir/TestRna.cpp.o -o ../TestRna -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 72%] Built target TestRna make -f tests/CMakeFiles/TestSanityDuMM.dir/build.make tests/CMakeFiles/TestSanityDuMM.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestSanityDuMM.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestSanityDuMM.dir/build.make tests/CMakeFiles/TestSanityDuMM.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 73%] Building CXX object tests/CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -MF CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o.d -o CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -c /<>/tests/TestSanityDuMM.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestSanityDuMM.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Linking CXX executable ../TestSanityDuMM cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSanityDuMM.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -o ../TestSanityDuMM -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 74%] Built target TestSanityDuMM make -f tests/CMakeFiles/TestSerine.dir/build.make tests/CMakeFiles/TestSerine.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestSerine.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestSerine.dir/build.make tests/CMakeFiles/TestSerine.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 75%] Building CXX object tests/CMakeFiles/TestSerine.dir/TestSerine.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestSerine.dir/TestSerine.cpp.o -MF CMakeFiles/TestSerine.dir/TestSerine.cpp.o.d -o CMakeFiles/TestSerine.dir/TestSerine.cpp.o -c /<>/tests/TestSerine.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestSerine.cpp:36: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Linking CXX executable ../TestSerine cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSerine.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSerine.dir/TestSerine.cpp.o -o ../TestSerine -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 75%] Built target TestSerine make -f tests/CMakeFiles/TestSetTorsion.dir/build.make tests/CMakeFiles/TestSetTorsion.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestSetTorsion.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestSetTorsion.dir/build.make tests/CMakeFiles/TestSetTorsion.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 76%] Building CXX object tests/CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -MF CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o.d -o CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -c /<>/tests/TestSetTorsion.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestSetTorsion.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 77%] Linking CXX executable ../TestSetTorsion cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSetTorsion.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -o ../TestSetTorsion -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 77%] Built target TestSetTorsion make -f tests/CMakeFiles/TestShortPdbLines.dir/build.make tests/CMakeFiles/TestShortPdbLines.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestShortPdbLines.dir/build.make tests/CMakeFiles/TestShortPdbLines.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 78%] Building CXX object tests/CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o -MF CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o.d -o CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o -c /<>/tests/TestShortPdbLines.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestShortPdbLines.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Linking CXX executable ../TestShortPdbLines cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestShortPdbLines.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o -o ../TestShortPdbLines -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 78%] Built target TestShortPdbLines make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 78%] Building CXX object tests/CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -MF CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o.d -o CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -c /<>/tests/TestTinkerAmber.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestTinkerAmber.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Linking CXX executable ../TestTinkerAmber cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTinkerAmber.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -o ../TestTinkerAmber -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 79%] Built target TestTinkerAmber make -f tests/CMakeFiles/TestTorsionPartitioner.dir/build.make tests/CMakeFiles/TestTorsionPartitioner.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestTorsionPartitioner.dir/build.make tests/CMakeFiles/TestTorsionPartitioner.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 80%] Building CXX object tests/CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -MF CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o.d -o CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -c /<>/tests/TestTorsionPartitioner.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestTorsionPartitioner.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Linking CXX executable ../TestTorsionPartitioner cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTorsionPartitioner.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -o ../TestTorsionPartitioner -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 81%] Built target TestTorsionPartitioner make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 82%] Building CXX object tests/CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -MF CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o.d -o CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -c /<>/tests/TestVelocityRescalingThermostat.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestVelocityRescalingThermostat.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Linking CXX executable ../TestVelocityRescalingThermostat cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestVelocityRescalingThermostat.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -o ../TestVelocityRescalingThermostat -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 83%] Built target TestVelocityRescalingThermostat make -f tests/CMakeFiles/TestWriteDefaultPdb.dir/build.make tests/CMakeFiles/TestWriteDefaultPdb.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestWriteDefaultPdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestWriteDefaultPdb.dir/build.make tests/CMakeFiles/TestWriteDefaultPdb.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 83%] Building CXX object tests/CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -MF CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o.d -o CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -c /<>/tests/TestWriteDefaultPdb.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestWriteDefaultPdb.cpp:2: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Linking CXX executable ../TestWriteDefaultPdb cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteDefaultPdb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -o ../TestWriteDefaultPdb -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 84%] Built target TestWriteDefaultPdb make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.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" /<> /<>/tests /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests /<>/obj-x86_64-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 85%] Building CXX object tests/CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -MF CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o.d -o CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -c /<>/tests/TestWriteSimtimePdb.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/TestWriteSimtimePdb.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Linking CXX executable ../TestWriteSimtimePdb cd /<>/obj-x86_64-linux-gnu/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteSimtimePdb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -o ../TestWriteSimtimePdb -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 86%] Built target TestWriteSimtimePdb make -f tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDrift.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 86%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -MF CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o.d -o CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -c /<>/tests/adhoc/RemoveMassCenterDrift.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/RemoveMassCenterDrift.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Linking CXX executable ../../RemoveMassCenterDrift cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/RemoveMassCenterDrift.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -o ../../RemoveMassCenterDrift -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 87%] Built target RemoveMassCenterDrift make -f tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 88%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o -MF CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o.d -o CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o -c /<>/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:8: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Linking CXX executable ../../RemoveMassCenterDriftWithOptimizer cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o -o ../../RemoveMassCenterDriftWithOptimizer -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 89%] Built target RemoveMassCenterDriftWithOptimizer make -f tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build.make tests/adhoc/CMakeFiles/TestEthaneFromSimbody.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build.make tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 90%] Building CXX object tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -MF CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o.d -o CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -c /<>/tests/adhoc/TestEthaneFromSimbody.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/TestEthaneFromSimbody.cpp:37: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Linking CXX executable ../../TestEthaneFromSimbody cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthaneFromSimbody.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -o ../../TestEthaneFromSimbody -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 91%] Built target TestEthaneFromSimbody make -f tests/adhoc/CMakeFiles/TestMemoryUse.dir/build.make tests/adhoc/CMakeFiles/TestMemoryUse.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestMemoryUse.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestMemoryUse.dir/build.make tests/adhoc/CMakeFiles/TestMemoryUse.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 91%] Building CXX object tests/adhoc/CMakeFiles/TestMemoryUse.dir/TestMemoryUse.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestMemoryUse.dir/TestMemoryUse.cpp.o -MF CMakeFiles/TestMemoryUse.dir/TestMemoryUse.cpp.o.d -o CMakeFiles/TestMemoryUse.dir/TestMemoryUse.cpp.o -c /<>/tests/adhoc/TestMemoryUse.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/TestMemoryUse.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /<>/tests/adhoc/TestMemoryUse.cpp: In function ‘size_t memory_used(bool)’: /<>/tests/adhoc/TestMemoryUse.cpp:36:25: warning: format ‘%u’ expects argument of type ‘unsigned int*’, but argument 3 has type ‘long unsigned int*’ [-Wformat=] 36 | fscanf (file, "%ul", &vm); // Just need the first num: vm size | ~^ ~~~ | | | | | long unsigned int* | unsigned int* | %lu /<>/tests/adhoc/TestMemoryUse.cpp:36:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | fscanf (file, "%ul", &vm); // Just need the first num: vm size | ~~~~~~~^~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX executable ../../TestMemoryUse cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMemoryUse.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestMemoryUse.dir/TestMemoryUse.cpp.o -o ../../TestMemoryUse -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 92%] Built target TestMemoryUse make -f tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSerineWithViz.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestSerineWithViz.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 93%] Building CXX object tests/adhoc/CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -MF CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o.d -o CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -c /<>/tests/adhoc/TestSerineWithViz.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/TestSerineWithViz.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Linking CXX executable ../../TestSerineWithViz cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSerineWithViz.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -o ../../TestSerineWithViz -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 94%] Built target TestSerineWithViz make -f tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build.make tests/adhoc/CMakeFiles/TestSimpleProtein.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestSimpleProtein.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build.make tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 95%] Building CXX object tests/adhoc/CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -MF CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o.d -o CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -c /<>/tests/adhoc/TestSimpleProtein.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/adhoc/TestSimpleProtein.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Linking CXX executable ../../TestSimpleProtein cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSimpleProtein.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -o ../../TestSimpleProtein -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 96%] Built target TestSimpleProtein make -f tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSodiumWithViz.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 97%] Building CXX object tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o -MF CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o.d -o CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o -c /<>/tests/adhoc/TestSodiumWithViz.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/tests/adhoc/TestSodiumWithViz.cpp:32: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/SimTKmolmodel.h:47: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Linking CXX executable ../../TestSodiumWithViz cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSodiumWithViz.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o -o ../../TestSodiumWithViz -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 98%] Built target TestSodiumWithViz make -f tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build.make tests/adhoc/CMakeFiles/TestWriteLargerPdb.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" /<> /<>/tests/adhoc /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/adhoc /<>/obj-x86_64-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build.make tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 99%] Building CXX object tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/x86_64-linux-gnu-g++ -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I/<>/src -I/<>/./include -isystem /usr/include/simbody -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o -MF CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o.d -o CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o -c /<>/tests/adhoc/TestWriteLargerPdb.cpp In file included from /<>/./include/SimTKmolmodel.h:51, from /<>/./include/Molmodel.h:45, from /<>/tests/adhoc/TestWriteLargerPdb.cpp:1: /<>/./include/molmodel/internal/AtomSubsystem.h:180:23: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 180 | : public std::iterator > | ^~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/12/bits/stl_algobase.h:65, from /usr/x86_64-linux-gnu/include/c++/12/bits/specfun.h:45, from /usr/x86_64-linux-gnu/include/c++/12/cmath:1935, from /usr/include/simbody/SimTKcommon/internal/common.h:255, from /usr/include/simbody/SimTKcommon/basics.h:38, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /<>/./include/Molmodel.h:44: /usr/x86_64-linux-gnu/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable ../../TestWriteLargerPdb cd /<>/obj-x86_64-linux-gnu/tests/adhoc && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteLargerPdb.dir/link.txt --verbose=1 /usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o -o ../../TestWriteLargerPdb -Wl,-rpath,/<>/obj-x86_64-linux-gnu ../../libSimTKmolmodel.so.3.0 /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 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target TestWriteLargerPdb 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' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-x86_64-linux-gnu && make -j1 install DESTDIR=/<>/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 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/doc/api/Molmodel/html -- Installing: /<>/debian/tmp/usr/doc/MolmodelAPI.html -- Installing: /<>/debian/tmp/usr/include/Molmodel.h -- Installing: /<>/debian/tmp/usr/include/SimTKmolmodel.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/AtomSubsystem.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Biotype.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Clonable.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Compound.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/CompoundModeler.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/CompoundSystem.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/DNA.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/DuMMForceFieldSubsystem.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Element.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Exceptions.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/GrinPointer.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Ions.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Ligands.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Linkage.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/MassCenterMotionRemover.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/MolecularMechanicsSystem.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/NA.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/NoseHooverThermostat.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/PDBReader.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Pdb.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/PeriodicPdbWriter.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/PeriodicVmdReporter.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Protein.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/RNA.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/RiboseMobilizer.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Superpose.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/VanDerWaalsForce.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/VanderWallSphere.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/VelocityRescalingThermostat.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/VmdConnection.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/VoxelHash.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/Water.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/bondGeometry.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/common.h -- Installing: /<>/debian/tmp/usr/include/molmodel/internal/units.h -- Installing: /<>/debian/tmp/usr/doc/MolmodelUsersGuide.pdf -- Installing: /<>/debian/tmp/usr/lib/libSimTKmolmodel.so.3.0 -- Installing: /<>/debian/tmp/usr/lib/libSimTKmolmodel.so make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install dh_install -plibsimtkmolmodel3.0 debian/tmp/usr/lib/libSimTKmolmodel.so.* usr/lib/x86_64-linux-gnu dh_install -plibsimtkmolmodel-dev debian/tmp/usr/lib/libSimTKmolmodel.so usr/lib/x86_64-linux-gnu rm -rf debian/tmp/usr/examples # not installing examples for now make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.0.113.gd05a5b6-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel3.0' in '../libsimtkmolmodel3.0_3.0.113.gd05a5b6-2_amd64.deb'. dpkg-deb: building package 'libsimtkmolmodel3.0-dbgsym' in '../libsimtkmolmodel3.0-dbgsym_3.0.113.gd05a5b6-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../molmodel_3.0.113.gd05a5b6-2_amd64.buildinfo dpkg-genchanges --build=any -O../molmodel_3.0.113.gd05a5b6-2_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-08-22T04:54:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ molmodel_3.0.113.gd05a5b6-2_amd64.changes: ------------------------------------------ Format: 1.8 Date: Mon, 30 May 2022 09:08:42 -0400 Source: molmodel Binary: libsimtkmolmodel-dev libsimtkmolmodel3.0 libsimtkmolmodel3.0-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 3.0.113.gd05a5b6-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libsimtkmolmodel-dev - C++ API for creating molecular models for SimTK (development file libsimtkmolmodel3.0 - C++ API for creating molecular models for SimTK Closes: 1009402 Changes: molmodel (3.0.113.gd05a5b6-2) unstable; urgency=medium . * Remove CMAKE_CXX_STANDARD setting (Closes: #1009402). * Bump copyright years. * Set upstream metadata fields: Bug-Database, Bug-Submit. * Update standards version to 4.6.0, no changes needed. 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5.1-6.1+b1), binutils (= 2.38.90.20220713-2), binutils-aarch64-linux-gnu (= 2.38.90.20220713-2), binutils-common (= 2.38.90.20220713-2), bsdextrautils (= 2.38.1-1), bsdutils (= 1:2.38.1-1), build-essential (= 12.9), bzip2 (= 1.0.8-5), cmake (= 3.24.1-1), cmake-data (= 3.24.1-1), coreutils (= 8.32-4.1), cpp (= 4:12.1.0-3), cpp-12 (= 12.1.0-8), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79), debhelper (= 13.9), debianutils (= 5.7-0.3), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.10), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dmsetup (= 2:1.02.185-1), dpkg (= 1.21.9), dpkg-dev (= 1.21.9), dwz (= 0.14-1), emacsen-common (= 3.0.4), file (= 1:5.41-4), findutils (= 4.9.0-3), freeglut3 (= 2.8.1-6), freeglut3-dev (= 2.8.1-6), g++ (= 4:12.1.0-3), g++-12 (= 12.1.0-8), gcc (= 4:12.1.0-3), gcc-12 (= 12.1.0-8), gcc-12-base (= 12.1.0-8), gemmi-dev (= 0.5.6+ds-1), gettext (= 0.21-8), gettext-base (= 0.21-8), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.12-1), hostname (= 3.23), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libapparmor1 (= 3.0.7-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.0-1), libargon2-1 (= 0~20171227-0.3), libasan8 (= 12.1.0-8), libatomic1 (= 12.1.0-8), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1+b1), libbinutils (= 2.38.90.20220713-2), libblas-dev (= 3.10.1-2), libblas3 (= 3.10.1-2), libblkid1 (= 2.38.1-1), libbrotli1 (= 1.0.9-2+b4), libbsd0 (= 0.11.6-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.34-4), libc-dev-bin (= 2.34-4), libc6 (= 2.34-4), libc6-dev (= 2.34-4), libcap-ng0 (= 0.8.3-1+b1), libcap2 (= 1:2.44-1), libcc1-0 (= 12.1.0-8), libcom-err2 (= 1.46.5-2), libcrypt-dev (= 1:4.4.28-2), libcrypt1 (= 1:4.4.28-2), libcryptsetup12 (= 2:2.5.0-2), libctf-nobfd0 (= 2.38.90.20220713-2), libctf0 (= 2.38.90.20220713-2), libcurl4 (= 7.84.0-2), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.264), libdebhelper-perl (= 13.9), libdevmapper1.02.1 (= 2:1.02.185-1), libdpkg-perl (= 1.21.9), libdrm-amdgpu1 (= 2.4.112-3), libdrm-common (= 2.4.112-3), libdrm-nouveau2 (= 2.4.112-3), libdrm-radeon1 (= 2.4.112-3), libdrm2 (= 2.4.112-3), libedit2 (= 3.1-20210910-1), libegl-dev (= 1.4.0-1), libegl-mesa0 (= 22.2.0~rc2-1), libegl1 (= 1.4.0-1), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libfdisk1 (= 2.38.1-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libgbm1 (= 22.2.0~rc2-1), libgcc-12-dev (= 12.1.0-8), libgcc-s1 (= 12.1.0-8), libgcrypt20 (= 1.10.1-2), libgdbm-compat4 (= 1.23-1+b1), libgdbm6 (= 1.23-1+b1), libgfortran5 (= 12.1.0-8), libgl-dev (= 1.4.0-1), libgl1 (= 1.4.0-1), libgl1-mesa-dev (= 22.2.0~rc2-1), libgl1-mesa-dri (= 22.2.0~rc2-1), libglapi-mesa (= 22.2.0~rc2-1), libgles-dev (= 1.4.0-1), libgles1 (= 1.4.0-1), libgles2 (= 1.4.0-1), libglu1-mesa (= 9.0.2-1), libglu1-mesa-dev (= 9.0.2-1), libglvnd-core-dev (= 1.4.0-1), libglvnd-dev (= 1.4.0-1), libglvnd0 (= 1.4.0-1), libglx-dev (= 1.4.0-1), libglx-mesa0 (= 22.2.0~rc2-1), libglx0 (= 1.4.0-1), libgmp10 (= 2:6.2.1+dfsg1-1), libgnutls30 (= 3.7.7-2), libgomp1 (= 12.1.0-8), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.90.20220713-2), libgssapi-krb5-2 (= 1.20-1), libhogweed6 (= 3.8.1-2), libice-dev (= 2:1.0.10-1), libice6 (= 2:1.0.10-1), libicu71 (= 71.1-3), libidn2-0 (= 2.3.3-1), libip4tc2 (= 1.8.8-1), libisl23 (= 0.25-1), libitm1 (= 12.1.0-8), libjson-c5 (= 0.16-1), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.3-1), libkmod2 (= 30+20220630-3), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), liblapack-dev (= 3.10.1-2), liblapack3 (= 3.10.1-2), libldap-2.5-0 (= 2.5.12+dfsg-2+b1), libllvm14 (= 1:14.0.6-2), liblsan0 (= 12.1.0-8), liblz4-1 (= 1.9.3-2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmmdb2-0 (= 2.0.22-1), libmmdb2-dev (= 2.0.22-1), libmount1 (= 2.38.1-1), libmpc3 (= 1.2.1-2), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.48.0-2), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libopengl-dev (= 1.4.0-1), libopengl0 (= 1.4.0-1), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.5.2-2), libpam-modules-bin (= 1.5.2-2), libpam-runtime (= 1.5.2-2), libpam0g (= 1.5.2-2), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-5), libpipeline1 (= 1.5.6-2), libprocps8 (= 2:3.3.17-7+b1), libpsl5 (= 0.21.0-1.2), libpthread-stubs0-dev (= 0.4-1), libquadmath0 (= 12.1.0-8), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.28+dfsg-7), libsasl2-modules-db (= 2.1.28+dfsg-7), libseccomp2 (= 2.5.4-1+b1), libselinux1 (= 3.4-1+b1), libsemanage-common (= 3.4-1), libsemanage2 (= 3.4-1+b1), libsensors-config (= 1:3.6.0-7), libsensors5 (= 1:3.6.0-7), libsepol2 (= 3.4-2), libsimbody-dev (= 3.6.1+dfsg-7), libsimbody3.6 (= 3.6.1+dfsg-7), libsm-dev (= 2:1.2.3-1), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.38.1-1), libssh2-1 (= 1.10.0-3+b1), libssl3 (= 3.0.5-2), libstdc++-12-dev (= 12.1.0-8), libstdc++6 (= 12.1.0-8), libsub-override-perl (= 0.09-3), libsystemd-shared (= 251.4-1), libsystemd0 (= 251.4-1), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libtsan2 (= 12.1.0-8), libubsan1 (= 12.1.0-8), libuchardet0 (= 0.0.7-1), libudev1 (= 251.4-1), libunistring2 (= 1.0-1), libuuid1 (= 2.38.1-1), libuv1 (= 1.44.2-1), libwayland-client0 (= 1.21.0-1), libwayland-server0 (= 1.21.0-1), libx11-6 (= 2:1.8.1-2), libx11-data (= 2:1.8.1-2), libx11-dev (= 2:1.8.1-2), libx11-xcb1 (= 2:1.8.1-2), libxau-dev (= 1:1.0.9-1), libxau6 (= 1:1.0.9-1), libxcb-dri2-0 (= 1.15-1), libxcb-dri3-0 (= 1.15-1), libxcb-glx0 (= 1.15-1), libxcb-present0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb-sync1 (= 1.15-1), libxcb-xfixes0 (= 1.15-1), libxcb1 (= 1.15-1), libxcb1-dev (= 1.15-1), libxdmcp-dev (= 1:1.1.2-3), libxdmcp6 (= 1:1.1.2-3), libxext-dev (= 2:1.3.4-1), libxext6 (= 2:1.3.4-1), libxfixes-dev (= 1:6.0.0-1), libxfixes3 (= 1:6.0.0-1), libxi-dev (= 2:1.8-1), libxi6 (= 2:1.8-1), libxml2 (= 2.9.14+dfsg-1+b1), libxmu-dev (= 2:1.1.3-3), libxmu-headers (= 2:1.1.3-3), libxmu6 (= 2:1.1.3-3), libxshmfence1 (= 1.3-1), libxt-dev (= 1:1.2.1-1), libxt6 (= 1:1.2.1-1), libxxf86vm1 (= 1:1.1.4-1+b2), libz3-4 (= 4.8.12-1+b1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.18.16-1), login (= 1:4.11.1+dfsg1-2), lsb-base (= 11.2), m4 (= 1.4.19-1), make (= 4.3-4.1), man-db (= 2.10.2-2), mawk (= 1.3.4.20200120-3.1), mount (= 2.38.1-1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), passwd (= 1:4.11.1+dfsg1-2), patch (= 2.7.6-7), perl (= 5.34.0-5), perl-base (= 5.34.0-5), perl-modules-5.34 (= 5.34.0-5), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-7+b1), rpcsvc-proto (= 1.4.2-4), sed (= 4.8-1), sensible-utils (= 0.0.17), sgml-base (= 1.30), systemd (= 251.4-1), sysvinit-utils (= 3.04-1), tao-pegtl-dev (= 3.2.7-1), tar (= 1.34+dfsg-1), util-linux (= 2.38.1-1), util-linux-extra (= 2.38.1-1), x11-common (= 1:7.7+23), x11proto-dev (= 2022.1-1), xorg-sgml-doctools (= 1:1.11-1.1), xtrans-dev (= 1.4.0-1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-4.1), zlib1g-dev (= 1:1.2.11.dfsg-4.1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1653916122" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libsimtkmolmodel-dev_3.0.113.gd05a5b6-2_amd64.deb ------------------------------------------------- new Debian package, version 2.0. size 1859932 bytes: control archive=2132 bytes. 1178 bytes, 25 lines control 3218 bytes, 41 lines md5sums Package: libsimtkmolmodel-dev Source: molmodel Version: 3.0.113.gd05a5b6-2 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 2265 Depends: libsimtkmolmodel3.0 (= 3.0.113.gd05a5b6-2) Section: libdevel Priority: optional Multi-Arch: same Homepage: https://simtk.org/projects/molmodel Description: C++ API for creating molecular models for SimTK (development files) Provides C++ API for creating molecular models whose dynamics can be simulated using the SimTK Simbody library. Molmodel is a programmer's toolkit for building reduced-coordinate, yet still all-atom, models of large biopolymers such as proteins, RNA, and DNA. One can control the allowed mobility. By default, Molmodel builds torsion-coordinate models in which bond stretch and bend angles are rigid while bond torsion angles are mobile. But one is able to rigidify or free any subsets of the atoms, such as the rigid benzene ring. . Molmodel is a C++ API for biochemist-friendly molecular modeling that extends the Simbody API to simplify construction of high-performance articulated models of molecules. . This package contains development files. drwxr-xr-x root/root 0 2022-05-30 13:08 ./ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/include/ -rw-r--r-- root/root 3055 2021-08-27 07:52 ./usr/include/Molmodel.h -rw-r--r-- root/root 4277 2021-08-27 07:52 ./usr/include/SimTKmolmodel.h drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/include/molmodel/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/include/molmodel/internal/ -rw-r--r-- root/root 7528 2021-08-27 07:52 ./usr/include/molmodel/internal/AtomSubsystem.h -rw-r--r-- root/root 7496 2021-08-27 07:52 ./usr/include/molmodel/internal/Biotype.h -rw-r--r-- root/root 3009 2021-08-27 07:52 ./usr/include/molmodel/internal/Clonable.h -rw-r--r-- root/root 86359 2021-08-27 07:52 ./usr/include/molmodel/internal/Compound.h -rw-r--r-- root/root 7005 2021-08-27 07:52 ./usr/include/molmodel/internal/CompoundModeler.h -rw-r--r-- root/root 6082 2021-08-27 07:52 ./usr/include/molmodel/internal/CompoundSystem.h -rw-r--r-- root/root 22366 2021-08-27 07:52 ./usr/include/molmodel/internal/DNA.h -rw-r--r-- root/root 70215 2021-08-27 07:52 ./usr/include/molmodel/internal/DuMMForceFieldSubsystem.h -rw-r--r-- root/root 19995 2021-08-27 07:52 ./usr/include/molmodel/internal/Element.h -rw-r--r-- root/root 363 2021-08-27 07:52 ./usr/include/molmodel/internal/Exceptions.h -rw-r--r-- root/root 6143 2021-08-27 07:52 ./usr/include/molmodel/internal/GrinPointer.h -rw-r--r-- root/root 15223 2021-08-27 07:52 ./usr/include/molmodel/internal/Ions.h -rw-r--r-- root/root 16871 2021-08-27 07:52 ./usr/include/molmodel/internal/Ligands.h -rw-r--r-- root/root 780 2021-08-27 07:52 ./usr/include/molmodel/internal/Linkage.h -rw-r--r-- root/root 11934 2021-08-27 07:52 ./usr/include/molmodel/internal/MassCenterMotionRemover.h -rw-r--r-- root/root 9510 2021-08-27 07:52 ./usr/include/molmodel/internal/MolecularMechanicsSystem.h -rw-r--r-- root/root 13907 2021-08-27 07:52 ./usr/include/molmodel/internal/NA.h -rw-r--r-- root/root 3377 2021-08-27 07:52 ./usr/include/molmodel/internal/NoseHooverThermostat.h -rw-r--r-- root/root 4459 2021-08-27 07:52 ./usr/include/molmodel/internal/PDBReader.h -rw-r--r-- root/root 19573 2021-08-27 07:52 ./usr/include/molmodel/internal/Pdb.h -rw-r--r-- root/root 4301 2021-08-27 07:52 ./usr/include/molmodel/internal/PeriodicPdbWriter.h -rw-r--r-- root/root 3549 2021-08-27 07:52 ./usr/include/molmodel/internal/PeriodicVmdReporter.h -rw-r--r-- root/root 51009 2021-08-27 07:52 ./usr/include/molmodel/internal/Protein.h -rw-r--r-- root/root 38117 2021-08-27 07:52 ./usr/include/molmodel/internal/RNA.h -rw-r--r-- root/root 5122 2021-08-27 07:52 ./usr/include/molmodel/internal/RiboseMobilizer.h -rw-r--r-- root/root 8762 2021-08-27 07:52 ./usr/include/molmodel/internal/Superpose.h -rw-r--r-- root/root 13560 2021-08-27 07:52 ./usr/include/molmodel/internal/VanDerWaalsForce.h -rw-r--r-- root/root 477 2021-08-27 07:52 ./usr/include/molmodel/internal/VanderWallSphere.h -rw-r--r-- root/root 11619 2021-08-27 07:52 ./usr/include/molmodel/internal/VelocityRescalingThermostat.h -rw-r--r-- root/root 935 2021-08-27 07:52 ./usr/include/molmodel/internal/VmdConnection.h -rw-r--r-- root/root 4845 2021-08-27 07:52 ./usr/include/molmodel/internal/VoxelHash.h -rw-r--r-- root/root 2851 2021-08-27 07:52 ./usr/include/molmodel/internal/Water.h -rw-r--r-- root/root 3664 2021-08-27 07:52 ./usr/include/molmodel/internal/bondGeometry.h -rw-r--r-- root/root 4253 2021-08-27 07:52 ./usr/include/molmodel/internal/common.h -rw-r--r-- root/root 3429 2021-08-27 07:52 ./usr/include/molmodel/internal/units.h drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2022-05-30 13:08 ./usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so -> libSimTKmolmodel.so.3.0 drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel-dev/ -rw-r--r-- root/root 580 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel-dev/changelog.Debian.gz -rw-r--r-- root/root 1447 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel-dev/copyright drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel-dev/doc/ -rw-r--r-- root/root 241 2021-08-27 07:52 ./usr/share/doc/libsimtkmolmodel-dev/doc/MolmodelAPI.html -rw-r--r-- root/root 1787506 2021-08-27 07:52 ./usr/share/doc/libsimtkmolmodel-dev/doc/MolmodelUsersGuide.pdf.gz libsimtkmolmodel3.0-dbgsym_3.0.113.gd05a5b6-2_amd64.deb ------------------------------------------------------- new Debian package, version 2.0. size 13851084 bytes: control archive=560 bytes. 430 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libsimtkmolmodel3.0-dbgsym Source: molmodel Version: 3.0.113.gd05a5b6-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 14086 Depends: libsimtkmolmodel3.0 (= 3.0.113.gd05a5b6-2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libsimtkmolmodel3.0 Build-Ids: ae4514a9b4c6e5475e538b3515fa8114e2ea46fd drwxr-xr-x root/root 0 2022-05-30 13:08 ./ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/debug/.build-id/ae/ -rw-r--r-- root/root 14412904 2022-05-30 13:08 ./usr/lib/debug/.build-id/ae/4514a9b4c6e5475e538b3515fa8114e2ea46fd.debug drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel3.0-dbgsym -> libsimtkmolmodel3.0 libsimtkmolmodel3.0_3.0.113.gd05a5b6-2_amd64.deb ------------------------------------------------ new Debian package, version 2.0. size 640756 bytes: control archive=1168 bytes. 1157 bytes, 23 lines control 249 bytes, 3 lines md5sums 63 bytes, 1 lines shlibs 65 bytes, 2 lines triggers Package: libsimtkmolmodel3.0 Source: molmodel Version: 3.0.113.gd05a5b6-2 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 2055 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.0), libsimbody3.6, libstdc++6 (>= 11), zlib1g (>= 1:1.2.6) Section: libs Priority: optional Multi-Arch: same Homepage: https://simtk.org/projects/molmodel Description: C++ API for creating molecular models for SimTK Provides C++ API for creating molecular models whose dynamics can be simulated using the SimTK Simbody library. Molmodel is a programmer's toolkit for building reduced-coordinate, yet still all-atom, models of large biopolymers such as proteins, RNA, and DNA. One can control the allowed mobility. By default, Molmodel builds torsion-coordinate models in which bond stretch and bend angles are rigid while bond torsion angles are mobile. But one is able to rigidify or free any subsets of the atoms, such as the rigid benzene ring. . Molmodel is a C++ API for biochemist-friendly molecular modeling that extends the Simbody API to simplify construction of high-performance articulated models of molecules. drwxr-xr-x root/root 0 2022-05-30 13:08 ./ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 2090136 2022-05-30 13:08 ./usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.0 drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel3.0/ -rw-r--r-- root/root 580 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel3.0/changelog.Debian.gz -rw-r--r-- root/root 1447 2022-05-30 13:08 ./usr/share/doc/libsimtkmolmodel3.0/copyright lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [571 B] Get:5 copy:/<>/apt_archive ./ Packages [658 B] Fetched 2192 B in 0s (52.6 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl liblist-moreutils-xs-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:amd64 t1utils unzip 0 upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 14.1 MB of archives. After this operation, 52.6 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://mirror.einval.org/debian sid/main arm64 netbase all 6.3 [19.9 kB] Get:3 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1.2-1.2 [73.9 kB] Get:4 http://mirror.einval.org/debian sid/main arm64 openssl arm64 3.0.5-2 [1389 kB] Get:5 http://mirror.einval.org/debian sid/main arm64 ca-certificates all 20211016 [156 kB] Get:6 http://mirror.einval.org/debian sid/main arm64 diffstat arm64 1.64-1 [34.6 kB] Get:7 http://mirror.einval.org/debian sid/main arm64 libassuan0 arm64 2.5.5-4 [48.9 kB] Get:8 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1.2-1.2 [160 kB] Get:9 http://mirror.einval.org/debian sid/main arm64 gpgconf arm64 2.2.35-3 [570 kB] Get:10 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.39.2-1 [786 kB] Get:11 http://mirror.einval.org/debian sid/main arm64 gpg arm64 2.2.35-3 [916 kB] Get:12 http://mirror.einval.org/debian sid/main arm64 iso-codes all 4.11.0-1 [2834 kB] Get:13 http://mirror.einval.org/debian sid/main arm64 libaliased-perl all 0.34-2 [14.2 kB] Get:14 http://mirror.einval.org/debian sid/main arm64 libapt-pkg-perl arm64 0.1.40+b1 [69.2 kB] Get:15 http://mirror.einval.org/debian sid/main arm64 libb-hooks-op-check-perl arm64 0.22-2 [11.2 kB] Get:16 http://mirror.einval.org/debian sid/main arm64 libdynaloader-functions-perl all 0.003-2 [13.1 kB] Get:17 http://mirror.einval.org/debian sid/main arm64 libdevel-callchecker-perl arm64 0.008-1+b3 [15.8 kB] Get:18 http://mirror.einval.org/debian sid/main arm64 libparams-classify-perl arm64 0.015-2 [25.4 kB] Get:19 http://mirror.einval.org/debian sid/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://mirror.einval.org/debian sid/main arm64 libtry-tiny-perl all 0.31-1 [24.2 kB] Get:21 http://mirror.einval.org/debian sid/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-progressive-perl all 0.001013-2 [8044 B] Get:23 http://mirror.einval.org/debian sid/main arm64 libvariable-magic-perl arm64 0.62-2 [44.3 kB] Get:24 http://mirror.einval.org/debian sid/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://mirror.einval.org/debian sid/main arm64 libberkeleydb-perl arm64 0.64-1+b2 [120 kB] Get:26 http://mirror.einval.org/debian sid/main arm64 libcapture-tiny-perl all 0.48-1 [26.0 kB] Get:27 http://mirror.einval.org/debian sid/main arm64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get:28 http://mirror.einval.org/debian sid/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:29 http://mirror.einval.org/debian sid/main arm64 liburi-perl all 5.12-1 [93.7 kB] Get:30 http://mirror.einval.org/debian sid/main arm64 libhtml-parser-perl arm64 3.78-1 [103 kB] Get:31 http://mirror.einval.org/debian sid/main arm64 libcgi-pm-perl all 4.54-1 [224 kB] Get:32 http://mirror.einval.org/debian sid/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:33 http://mirror.einval.org/debian sid/main arm64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get:34 http://mirror.einval.org/debian sid/main arm64 libclass-xsaccessor-perl arm64 1.19-4 [36.3 kB] Get:35 http://mirror.einval.org/debian sid/main arm64 libclone-perl arm64 0.45-1+b2 [15.3 kB] Get:36 http://mirror.einval.org/debian sid/main arm64 libconfig-tiny-perl all 2.28-1 [17.3 kB] Get:37 http://mirror.einval.org/debian sid/main arm64 libparams-util-perl arm64 1.102-1+b2 [25.2 kB] Get:38 http://mirror.einval.org/debian sid/main arm64 libsub-install-perl all 0.928-2 [11.0 kB] Get:39 http://mirror.einval.org/debian sid/main arm64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:40 http://mirror.einval.org/debian sid/main arm64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:41 http://mirror.einval.org/debian sid/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://mirror.einval.org/debian sid/main arm64 libcpanel-json-xs-perl arm64 4.32-1 [128 kB] Get:43 http://mirror.einval.org/debian sid/main arm64 libdevel-stacktrace-perl all 2.0400-1 [28.6 kB] Get:44 http://mirror.einval.org/debian sid/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://mirror.einval.org/debian sid/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://mirror.einval.org/debian sid/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://mirror.einval.org/debian sid/main arm64 libexporter-tiny-perl all 1.002002-1 [37.8 kB] Get:48 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-xs-perl arm64 0.430-3 [36.7 kB] Get:49 http://mirror.einval.org/debian sid/main arm64 liblist-moreutils-perl all 0.430-2 [46.9 kB] Get:50 http://mirror.einval.org/debian sid/main arm64 libdata-dpath-perl all 0.58-1 [43.5 kB] Get:51 http://mirror.einval.org/debian sid/main arm64 libdata-messagepack-perl arm64 1.02-1 [34.6 kB] Get:52 http://mirror.einval.org/debian sid/main arm64 libnet-domain-tld-perl all 1.75-2 [33.7 kB] Get:53 http://mirror.einval.org/debian sid/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:54 http://mirror.einval.org/debian sid/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:55 http://mirror.einval.org/debian sid/main arm64 libnet-netmask-perl all 2.0001-1 [32.2 kB] Get:56 http://mirror.einval.org/debian sid/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2 [103 kB] Get:57 http://mirror.einval.org/debian sid/main arm64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:58 http://mirror.einval.org/debian sid/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:59 http://mirror.einval.org/debian sid/main arm64 libdevel-size-perl arm64 0.83-2 [25.7 kB] Get:60 http://mirror.einval.org/debian sid/main arm64 libemail-address-xs-perl arm64 1.05-1 [28.0 kB] Get:61 http://mirror.einval.org/debian sid/main arm64 libencode-locale-perl all 1.05-2 [13.5 kB] Get:62 http://mirror.einval.org/debian sid/main arm64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:63 http://mirror.einval.org/debian sid/main arm64 libfile-basedir-perl all 0.09-1 [16.4 kB] Get:64 http://mirror.einval.org/debian sid/main arm64 libnumber-compare-perl all 0.03-2 [7448 B] Get:65 http://mirror.einval.org/debian sid/main arm64 libtext-glob-perl all 0.11-2 [8992 B] Get:66 http://mirror.einval.org/debian sid/main arm64 libfile-find-rule-perl all 0.34-2 [28.4 kB] Get:67 http://mirror.einval.org/debian sid/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:68 http://mirror.einval.org/debian sid/main arm64 libhttp-date-perl all 6.05-1 [10.4 kB] Get:69 http://mirror.einval.org/debian sid/main arm64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:70 http://mirror.einval.org/debian sid/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:71 http://mirror.einval.org/debian sid/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:72 http://mirror.einval.org/debian sid/main arm64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get:73 http://mirror.einval.org/debian sid/main arm64 libhttp-message-perl all 6.37-1 [80.9 kB] Get:74 http://mirror.einval.org/debian sid/main arm64 libhtml-form-perl all 6.09-1 [23.3 kB] Get:75 http://mirror.einval.org/debian sid/main arm64 libhtml-html5-entities-perl all 0.004-2 [21.6 kB] Get:76 http://mirror.einval.org/debian sid/main arm64 libhtml-tree-perl all 5.07-2 [213 kB] Get:77 http://mirror.einval.org/debian sid/main arm64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:78 http://mirror.einval.org/debian sid/main arm64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:79 http://mirror.einval.org/debian sid/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get:80 http://mirror.einval.org/debian sid/main arm64 libnet-ssleay-perl arm64 1.92-2 [338 kB] Get:81 http://mirror.einval.org/debian sid/main arm64 libio-socket-ssl-perl all 2.074-2 [220 kB] Get:82 http://mirror.einval.org/debian sid/main arm64 libnet-http-perl all 6.22-1 [25.3 kB] Get:83 http://mirror.einval.org/debian sid/main arm64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:84 http://mirror.einval.org/debian sid/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:85 http://mirror.einval.org/debian sid/main arm64 libwww-perl all 6.67-1 [194 kB] Get:86 http://mirror.einval.org/debian sid/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:87 http://mirror.einval.org/debian sid/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:88 http://mirror.einval.org/debian sid/main arm64 libio-interactive-perl all 1.023-1 [11.5 kB] Get:89 http://mirror.einval.org/debian sid/main arm64 libipc-run3-perl all 0.048-2 [34.2 kB] Get:90 http://mirror.einval.org/debian sid/main arm64 libjson-maybexs-perl all 1.004003-1 [13.1 kB] Get:91 http://mirror.einval.org/debian sid/main arm64 liblist-compare-perl all 0.55-1 [66.9 kB] Get:92 http://mirror.einval.org/debian sid/main arm64 liblist-someutils-perl all 0.58-1 [36.5 kB] Get:93 http://mirror.einval.org/debian sid/main arm64 liblist-utilsby-perl all 0.12-1 [16.1 kB] Get:94 http://mirror.einval.org/debian sid/main arm64 liblz1 arm64 1.13-4 [40.8 kB] Get:95 http://mirror.einval.org/debian sid/main arm64 liblzo2-2 arm64 2.10-2 [51.8 kB] Get:96 http://mirror.einval.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2 [34.1 kB] Get:97 http://mirror.einval.org/debian sid/main arm64 libmldbm-perl all 2.05-3 [18.8 kB] Get:98 http://mirror.einval.org/debian sid/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:99 http://mirror.einval.org/debian sid/main arm64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:100 http://mirror.einval.org/debian sid/main arm64 libmoo-perl all 2.005004-3 [60.5 kB] Get:101 http://mirror.einval.org/debian sid/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:102 http://mirror.einval.org/debian sid/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:103 http://mirror.einval.org/debian sid/main arm64 libmouse-perl arm64 2.5.10-1+b2 [171 kB] Get:104 http://mirror.einval.org/debian sid/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:105 http://mirror.einval.org/debian sid/main arm64 libsub-identify-perl arm64 0.14-2 [11.9 kB] Get:106 http://mirror.einval.org/debian sid/main arm64 libsub-name-perl arm64 0.26-2 [13.5 kB] Get:107 http://mirror.einval.org/debian sid/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:108 http://mirror.einval.org/debian sid/main arm64 libpath-tiny-perl all 0.122-1 [56.0 kB] Get:109 http://mirror.einval.org/debian sid/main arm64 libperlio-gzip-perl arm64 0.20-1 [17.1 kB] Get:110 http://mirror.einval.org/debian sid/main arm64 libperlio-utf8-strict-perl arm64 0.009-1+b1 [11.9 kB] Get:111 http://mirror.einval.org/debian sid/main arm64 libproc-processtable-perl arm64 0.634-1+b1 [46.4 kB] Get:112 http://mirror.einval.org/debian sid/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:113 http://mirror.einval.org/debian sid/main arm64 libsereal-decoder-perl arm64 4.025+ds-1 [97.7 kB] Get:114 http://mirror.einval.org/debian sid/main arm64 libsereal-encoder-perl arm64 4.025+ds-1 [98.4 kB] Get:115 http://mirror.einval.org/debian sid/main arm64 libsort-versions-perl all 1.62-2 [10.7 kB] Get:116 http://mirror.einval.org/debian sid/main arm64 libxs-parse-keyword-perl arm64 0.25-1 [52.2 kB] Get:117 http://mirror.einval.org/debian sid/main arm64 libsyntax-keyword-try-perl arm64 0.27-1 [28.2 kB] Get:118 http://mirror.einval.org/debian sid/main arm64 libterm-readkey-perl arm64 2.38-2 [26.9 kB] Get:119 http://mirror.einval.org/debian sid/main arm64 libtext-levenshteinxs-perl arm64 0.03-5 [8704 B] Get:120 http://mirror.einval.org/debian sid/main arm64 libtext-markdown-discount-perl arm64 0.13-1+b1 [13.4 kB] Get:121 http://mirror.einval.org/debian sid/main arm64 libtext-xslate-perl arm64 3.5.9-1+b1 [194 kB] Get:122 http://mirror.einval.org/debian sid/main arm64 libtime-duration-perl all 1.21-1 [13.7 kB] Get:123 http://mirror.einval.org/debian sid/main arm64 libtime-moment-perl arm64 0.44-2 [72.5 kB] Get:124 http://mirror.einval.org/debian sid/main arm64 libunicode-utf8-perl arm64 0.62-1+b3 [19.8 kB] Get:125 http://mirror.einval.org/debian sid/main arm64 libwww-mechanize-perl all 2.14-2 [120 kB] Get:126 http://mirror.einval.org/debian sid/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get:127 http://mirror.einval.org/debian sid/main arm64 libyaml-libyaml-perl arm64 0.83+ds-1+b1 [34.4 kB] Get:128 http://mirror.einval.org/debian sid/main arm64 plzip arm64 1.10-4 [60.7 kB] Get:129 http://mirror.einval.org/debian sid/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:130 http://mirror.einval.org/debian sid/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:131 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:132 http://mirror.einval.org/debian sid/main arm64 unzip arm64 6.0-27 [163 kB] Get:133 http://mirror.einval.org/debian sid/main arm64 lintian all 2.115.2 [1416 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.1 MB in 0s (42.3 MB/s) Selecting previously unselected package netbase. (Reading database ... 25551 files and directories currently installed.) Preparing to unpack .../000-netbase_6.3_all.deb ... Unpacking netbase (6.3) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.1.2-1.2_all.deb ... Unpacking readline-common (8.1.2-1.2) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.5-2_arm64.deb ... Unpacking openssl (3.0.5-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.64-1_arm64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../005-libassuan0_2.5.5-4_arm64.deb ... Unpacking libassuan0:arm64 (2.5.5-4) ... Selecting previously unselected package libreadline8:arm64. 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Unpacking libapt-pkg-perl (0.1.40+b1) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (0.22-2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-2_all.deb ... Unpacking libdynaloader-functions-perl (0.003-2) ... Selecting previously unselected package libdevel-callchecker-perl. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-1+b3_arm64.deb ... Unpacking libdevel-callchecker-perl (0.008-1+b3) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../016-libparams-classify-perl_0.015-2_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... 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Unpacking sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b1) ... Setting up liblz1:arm64 (1.13-4) ... Setting up libberkeleydb-perl:arm64 (0.64-1+b2) ... Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-1+b3) ... Setting up libmouse-perl (2.5.10-1+b2) ... Setting up libdata-messagepack-perl (1.02-1) ... Setting up libdynaloader-functions-perl (0.003-2) ... Setting up libtext-glob-perl (0.11-2) ... Setting up libclass-method-modifiers-perl (2.13-1) ... Setting up liblist-compare-perl (0.55-1) ... Setting up libclone-perl (0.45-1+b2) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-2) ... Setting up libcpanel-json-xs-perl:arm64 (4.32-1) ... Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdevel-size-perl (0.83-2) ... Setting up unzip (6.0-27) ... Setting up libsqlite3-0:arm64 (3.39.2-1) ... Setting up liblwp-mediatypes-perl (6.04-1) ... Setting up libyaml-libyaml-perl (0.83+ds-1+b1) ... Setting up libio-interactive-perl (1.023-1) ... Setting up libtry-tiny-perl (0.31-1) ... Setting up perl-openssl-defaults:arm64 (7+b1) ... Setting up libmldbm-perl (2.05-3) ... Setting up liblzo2-2:arm64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2) ... Setting up libencode-locale-perl (1.05-2) ... Setting up libassuan0:arm64 (2.5.5-4) ... Setting up libconfig-tiny-perl (2.28-1) ... Setting up libsereal-encoder-perl:arm64 (4.025+ds-1) ... Setting up liblist-utilsby-perl (0.12-1) ... Setting up libnet-netmask-perl (2.0001-1) ... Setting up libsub-install-perl (0.928-2) ... Setting up libnumber-compare-perl (0.03-2) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004003-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.25-1) ... Setting up libfile-find-rule-perl (0.34-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-2) ... Setting up libperlio-utf8-strict-perl (0.009-1+b1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.62-2) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-2) ... Setting up liblist-moreutils-xs-perl (0.430-3) ... Setting up libparams-util-perl (1.102-1+b2) ... Setting up libtime-duration-perl (1.21-1) ... Setting up libtext-xslate-perl:arm64 (3.5.9-1+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-2) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl:arm64 (0.26-2) ... Setting up libsyntax-keyword-try-perl (0.27-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:arm64 (0.634-1+b1) ... Setting up libpath-tiny-perl (0.122-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-2) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-2) ... Setting up netbase (6.3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libdevel-stacktrace-perl (2.0400-1) ... Setting up libclass-xsaccessor-perl (1.19-4) ... Setting up libsort-versions-perl (1.62-2) ... Setting up libexporter-tiny-perl (1.002002-1) ... Setting up libterm-readkey-perl (2.38-2) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.5-2) ... Setting up libtext-levenshteinxs-perl (0.03-5) ... Setting up libperlio-gzip-perl (0.20-1) ... Setting up readline-common (8.1.2-1.2) ... Setting up libhtml-html5-entities-perl (0.004-2) ... Setting up libsereal-decoder-perl (4.025+ds-1) ... Setting up libmarkdown2:arm64 (2.2.7-2) ... Setting up liburi-perl (5.12-1) ... Setting up iso-codes (4.11.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.05-1) ... Setting up libnet-ssleay-perl:arm64 (1.92-2) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libfile-basedir-perl (0.09-1) ... Setting up libfile-listing-perl (6.15-1) ... Setting up liblist-moreutils-perl (0.430-2) ... Setting up libreadline8:arm64 (8.1.2-1.2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl:arm64 (0.13-1+b1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl (0.008-1+b3) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:arm64 (3.78-1) ... Setting up gpgconf (2.2.35-3) ... Setting up libio-socket-ssl-perl (2.074-2) ... Setting up gpg (2.2.35-3) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.37-1) ... Setting up libhtml-form-perl (6.09-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl:arm64 (0.015-2) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.14-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Processing triggers for libc-bin (2.34-4) ... Processing triggers for man-db (2.10.2-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for sgml-base (1.30) ... Setting up lintian (2.115.2) ... Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 713252 Build-Time: 2937 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 93 Job: molmodel_3.0.113.gd05a5b6-2 Lintian: pass Machine Architecture: arm64 Package: molmodel Package-Time: 3075 Source-Version: 3.0.113.gd05a5b6-2 Space: 713252 Status: successful Version: 3.0.113.gd05a5b6-2 -------------------------------------------------------------------------------- Finished at 2022-08-22T04:54:43Z Build needed 00:51:15, 713252k disk space