------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.53.txz ===== Message from ca_root_nss-3.53: -- 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_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/jsoncpp-1.9.2.txz Installing /packages/All/libuv-1.38.0.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-3.4.3,1.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/cmake-3.17.3.txz Installing /packages/All/hdf-szip-2.1.1.txz Installing /packages/All/hdf5-1.10.6,1.txz Installing /packages/All/htslib-1.9.txz SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.2_1 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.2_1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.46.2_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.2_1 for building ===> Extracting for kallisto-0.46.2_1 => SHA256 Checksum OK for pachterlab-kallisto-v0.46.2_GH0.tar.gz. Extracted Memory Use: 11.60M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for kallisto-0.46.2_1 ===> Applying ports patches for kallisto-0.46.2_1 from /xports/biology/kallisto/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> kallisto-0.46.2_1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> kallisto-0.46.2_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> kallisto-0.46.2_1 depends on file: /usr/local/bin/cmake - found ===> kallisto-0.46.2_1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> kallisto-0.46.2_1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> kallisto-0.46.2_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Configuring for kallisto-0.46.2_1 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/kallisto/.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 shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so (found version "1.10.6") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- 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 CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/kallisto/.build SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for kallisto-0.46.2_1 /usr/local/bin/cmake -S/construction/biology/kallisto/kallisto-0.46.2 -B/construction/biology/kallisto/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/kallisto/.build/CMakeFiles /construction/biology/kallisto/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/CMakeFiles/kallisto_core.dir/all --- /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend --- src/CMakeFiles/kallisto_core.dir/depend --- cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.2 /construction/biology/kallisto/kallisto-0.46.2/src /construction/biology/kallisto/.build /construction/biology/kallisto/.build/src /construction/biology/kallisto/.build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake Scanning dependencies of target kallisto_core /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build --- src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/Merge.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o --- --- src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o --- src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o --- src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/BUSTools.cpp --- src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/Bootstrap.cpp --- src/CMakeFiles/kallisto_core.dir/Merge.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o --- src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o --- src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o --- [ 27%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o --- src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/BUSData.cpp --- src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o --- [ 31%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o --- src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o --- [ 36%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o --- src/CMakeFiles/kallisto_core.dir/Merge.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/Merge.cpp --- src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/KmerIterator.cpp --- src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/Kmer.cpp --- src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/MinCollector.cpp --- src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/KmerIndex.cpp --- src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o --- [ 40%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/H5Writer.cpp --- src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o --- [ 45%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/GeneModel.cpp --- src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o --- [ 50%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/PlaintextWriter.cpp --- src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o --- [ 54%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/ProcessReads.cpp --- src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o --- [ 59%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/PseudoBam.cpp --- src/CMakeFiles/kallisto_core.dir/common.cpp.o --- [ 63%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/common.cpp --- src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o --- [ 68%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/h5utils.cpp --- src/CMakeFiles/kallisto_core.dir/hash.cpp.o --- [ 72%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/hash.cpp --- src/CMakeFiles/kallisto_core.dir/main.cpp.o --- [ 77%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/main.cpp --- src/CMakeFiles/kallisto_core.dir/weights.cpp.o --- [ 81%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/weights.cpp --- src/libkallisto_core.a --- [ 86%] Linking CXX static library libkallisto_core.a cd /construction/biology/kallisto/.build/src && /usr/local/bin/cmake -P CMakeFiles/kallisto_core.dir/cmake_clean_target.cmake cd /construction/biology/kallisto/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kallisto_core.dir/link.txt --verbose=1 /usr/bin/ar qc libkallisto_core.a CMakeFiles/kallisto_core.dir/BUSData.cpp.o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o CMakeFiles/kallisto_core.dir/Kmer.cpp.o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o CMakeFiles/kallisto_core.dir/Merge.cpp.o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o CMakeFiles/kallisto_core.dir/common.cpp.o CMakeFiles/kallisto_core.dir/h5utils.cpp.o CMakeFiles/kallisto_core.dir/hash.cpp.o CMakeFiles/kallisto_core.dir/main.cpp.o CMakeFiles/kallisto_core.dir/weights.cpp.o /usr/bin/ranlib libkallisto_core.a [ 86%] Built target kallisto_core --- src/CMakeFiles/kallisto.dir/all --- /usr/bin/make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend --- src/CMakeFiles/kallisto.dir/depend --- cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.2 /construction/biology/kallisto/kallisto-0.46.2/src /construction/biology/kallisto/.build /construction/biology/kallisto/.build/src /construction/biology/kallisto/.build/src/CMakeFiles/kallisto.dir/DependInfo.cmake Scanning dependencies of target kallisto /usr/bin/make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build --- src/CMakeFiles/kallisto.dir/main.cpp.o --- [ 90%] Building CXX object src/CMakeFiles/kallisto.dir/main.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -DUSE_HDF5=ON -I/construction/biology/kallisto/kallisto-0.46.2/src -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 -std=c++11 -o CMakeFiles/kallisto.dir/main.cpp.o -c /construction/biology/kallisto/kallisto-0.46.2/src/main.cpp --- src/kallisto --- [ 95%] Linking CXX executable kallisto cd /construction/biology/kallisto/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/link.txt --verbose=1 /usr/bin/c++ -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 -L/usr/local/lib CMakeFiles/kallisto.dir/main.cpp.o -o kallisto -Wl,-z,origin,-rpath,/usr/local/lib libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz /usr/local/lib/libhdf5.so /usr/local/lib/libsz.so -lz -ldl -lm -lrt [100%] Built target kallisto /usr/local/bin/cmake -E cmake_progress_start /construction/biology/kallisto/.build/CMakeFiles 0 SUCCEEDED 00:01:13 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for kallisto-0.46.2_1 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/kallisto/kallisto-0.46.2 -B/construction/biology/kallisto/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/kallisto/.build/CMakeFiles /construction/biology/kallisto/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.2 /construction/biology/kallisto/kallisto-0.46.2/src /construction/biology/kallisto/.build /construction/biology/kallisto/.build/src /construction/biology/kallisto/.build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build [ 86%] Built target kallisto_core /usr/bin/make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.2 /construction/biology/kallisto/kallisto-0.46.2/src /construction/biology/kallisto/.build /construction/biology/kallisto/.build/src /construction/biology/kallisto/.build/src/CMakeFiles/kallisto.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/build [100%] Built target kallisto /usr/local/bin/cmake -E cmake_progress_start /construction/biology/kallisto/.build/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall /usr/bin/make -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/preinstall Linking CXX executable CMakeFiles/CMakeRelink.dir/kallisto cd /construction/biology/kallisto/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kallisto.dir/relink.txt --verbose=1 /usr/bin/c++ -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 -L/usr/local/lib CMakeFiles/kallisto.dir/main.cpp.o -o CMakeFiles/CMakeRelink.dir/kallisto -Wl,-z,origin,-rpath,/usr/local/lib libkallisto_core.a -lpthread -lhts libkallisto_core.a -lz /usr/local/lib/libhdf5.so /usr/local/lib/libsz.so -lz -ldl -lm -lrt Installing the project stripped... /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /construction/biology/kallisto/stage/usr/local/bin/kallisto install -m 555 /construction/biology/kallisto/kallisto-test /construction/biology/kallisto/stage/usr/local/bin cd /construction/biology/kallisto/kallisto-0.46.2/test && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/kallisto/stage/usr/local/share/examples/kallisto ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for kallisto-0.46.2_1 file sizes/checksums [11]: 0% file sizes/checksums [11]: 100% packing files [11]: 0% packing files [11]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:01:36