------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/libnghttp2-1.40.0.txz Installing /packages/All/ca_root_nss-3.52.txz ===== Message from ca_root_nss-3.52: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/curl-7.70.0.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/jsoncpp-1.9.2.txz Installing /packages/All/libuv-1.37.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/rhash-1.3.9.txz Installing /packages/All/liblz4-1.9.2_1,1.txz Installing /packages/All/lzo2-2.10_1.txz Installing /packages/All/libarchive-3.4.2,1.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/cmake-3.17.2.txz Installing /packages/All/maeparser-1.2.3.txz SUCCEEDED 00:00:18 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/sbin/pkg - found => schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/schrodinger/coordgenlibs/tar.gz/v1.4.0-6-g95e2367?dummy=/schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz fetch: https://codeload.github.com/schrodinger/coordgenlibs/tar.gz/v1.4.0-6-g95e2367?dummy=/schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz: size unknown fetch: https://codeload.github.com/schrodinger/coordgenlibs/tar.gz/v1.4.0-6-g95e2367?dummy=/schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz: size of remote file is not known schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0 0 B 0 Bps schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0 48 kB 396 kBps schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0 151 kB 619 kBps 01s ===> Fetching all distfiles required by coordgenlibs-1.4.0.6 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by coordgenlibs-1.4.0.6 for building => SHA256 Checksum OK for schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by coordgenlibs-1.4.0.6 for building ===> Extracting for coordgenlibs-1.4.0.6 => SHA256 Checksum OK for schrodinger-coordgenlibs-v1.4.0-6-g95e2367_GH0.tar.gz. Extracted Memory Use: 1.02M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for coordgenlibs-1.4.0.6 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/include/boost/dynamic_bitset.hpp - found ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/include/boost/dynamic_bitset.hpp - found ===> coordgenlibs-1.4.0.6 depends on file: /usr/local/bin/cmake - found ===> coordgenlibs-1.4.0.6 depends on shared library: libmaeparser.so - found (/usr/local/lib/libmaeparser.so) ===> Configuring for coordgenlibs-1.4.0.6 ===> Performing out-of-source build /bin/mkdir -p /construction/science/coordgenlibs/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc - works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- maeparser include dir set as '/usr/local/include' -- maeparser libraries set as '/usr/local/lib/libmaeparser.so' -- Found compiled maeparser library at -- Found Boost: /usr/local/include (found version "1.72.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/science/coordgenlibs/.build SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for coordgenlibs-1.4.0.6 /usr/local/bin/cmake -S/construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367 -B/construction/science/coordgenlibs/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/science/coordgenlibs/.build/CMakeFiles /construction/science/coordgenlibs/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/coordgen.dir/all --- /usr/bin/make -f CMakeFiles/coordgen.dir/build.make CMakeFiles/coordgen.dir/depend --- CMakeFiles/coordgen.dir/depend --- cd /construction/science/coordgenlibs/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367 /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367 /construction/science/coordgenlibs/.build /construction/science/coordgenlibs/.build /construction/science/coordgenlibs/.build/CMakeFiles/coordgen.dir/DependInfo.cmake Scanning dependencies of target coordgen /usr/bin/make -f CMakeFiles/coordgen.dir/build.make CMakeFiles/coordgen.dir/build --- CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o --- --- CMakeFiles/coordgen.dir/CoordgenFragmenter.cpp.o --- --- CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o --- --- CMakeFiles/coordgen.dir/CoordgenMinimizer.cpp.o --- --- CMakeFiles/coordgen.dir/CoordgenTemplates.cpp.o --- --- CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o --- --- CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o --- --- CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o --- --- CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o --- --- CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o --- --- CMakeFiles/coordgen.dir/CoordgenFragmenter.cpp.o --- [ 6%] Building CXX object CMakeFiles/coordgen.dir/CoordgenFragmenter.cpp.o --- CMakeFiles/coordgen.dir/CoordgenTemplates.cpp.o --- [ 12%] Building CXX object CMakeFiles/coordgen.dir/CoordgenTemplates.cpp.o --- CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o --- [ 18%] Building CXX object CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o --- CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o --- [ 31%] Building CXX object CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o --- CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o --- [ 31%] Building CXX object CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o --- CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o --- [ 43%] Building CXX object CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o --- CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o --- [ 43%] Building CXX object CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o --- CMakeFiles/coordgen.dir/CoordgenTemplates.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS 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-fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/sketcherMinimizerAtom.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/sketcherMinimizerAtom.cpp --- CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o --- [ 50%] Building CXX object CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o --- CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/CoordgenFragmentBuilder.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/CoordgenFragmentBuilder.cpp --- CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o --- [ 56%] Building CXX object CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o --- CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/sketcherMinimizer.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/sketcherMinimizer.cpp --- CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/sketcherMinimizerFragment.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/sketcherMinimizerFragment.cpp --- CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/sketcherMinimizerBond.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/sketcherMinimizerBond.cpp --- CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/CoordgenMacrocycleBuilder.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/CoordgenMacrocycleBuilder.cpp --- CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o --- /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -fvisibility=hidden -std=gnu++11 -o CMakeFiles/coordgen.dir/sketcherMinimizerMarchingSquares.cpp.o -c /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/sketcherMinimizerMarchingSquares.cpp --- CMakeFiles/coordgen.dir/CoordgenMinimizer.cpp.o --- [ 62%] Building CXX object CMakeFiles/coordgen.dir/CoordgenMinimizer.cpp.o /usr/bin/c++ -DIN_COORDGEN -DUSE_MAEPARSER -Dcoordgen_EXPORTS -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include 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CMakeFiles/coordgen.dir/sketcherMinimizerRing.cpp.o -lmaeparser /usr/local/bin/cmake -E cmake_symlink_library CMakeFiles/CMakeRelink.dir/libcoordgen.so.1.4.0 CMakeFiles/CMakeRelink.dir/libcoordgen.so.1 CMakeFiles/CMakeRelink.dir/libcoordgen.so Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/science/coordgenlibs/stage/usr/local/lib/libcoordgen.so.1.4.0 -- Installing: /construction/science/coordgenlibs/stage/usr/local/lib/libcoordgen.so.1 -- Installing: /construction/science/coordgenlibs/stage/usr/local/lib/libcoordgen.so -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/CoordgenConfig.hpp -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/CoordgenFragmentBuilder.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/CoordgenFragmenter.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/CoordgenMacrocycleBuilder.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/CoordgenMinimizer.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerAtom.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerBendInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerBond.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerClashInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerEZConstrainInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerFragment.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizer.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerMarchingSquares.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerMaths.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerMolecule.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerResidue.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerResidueInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerRing.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/include/coordgen/sketcherMinimizerStretchInteraction.h -- Installing: /construction/science/coordgenlibs/stage/usr/local/lib/cmake/coordgen-config.cmake -- Installing: /construction/science/coordgenlibs/stage/usr/local/lib/cmake/coordgen-config-release.cmake /bin/mkdir -p /construction/science/coordgenlibs/stage/usr/local/share/coordgen install -m 0644 /construction/science/coordgenlibs/coordgenlibs-1.4.0-6-g95e2367/templates.mae /construction/science/coordgenlibs/stage/usr/local/share/coordgen ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/libcoordgen.so.1.4.0 is linked to /usr/local/lib/libboost_iostreams.so.1.72.0 from devel/boost-libs but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libboost_iostreams.so:devel/boost-libs Error: /usr/local/lib/libcoordgen.so.1.4.0 is linked to /usr/local/lib/libboost_regex.so.1.72.0 from devel/boost-libs but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libboost_regex.so:devel/boost-libs Error: /usr/local/lib/libcoordgen.so.1.4.0 is linked to /usr/local/lib/libicudata.so.67 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicudata.so:devel/icu Error: /usr/local/lib/libcoordgen.so.1.4.0 is linked to /usr/local/lib/libicui18n.so.67 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicui18n.so:devel/icu Error: /usr/local/lib/libcoordgen.so.1.4.0 is linked to /usr/local/lib/libicuuc.so.67 from devel/icu but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libicuuc.so:devel/icu Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for coordgenlibs-1.4.0.6 file sizes/checksums [26]: 0% file sizes/checksums [26]: 100% packing files [26]: 0% packing files [26]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:55