------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.32.0.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- 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-7.72.0.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/libuv-1.39.0.txz Installing /packages/All/gettext-runtime-0.21.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-6.2.20200831.txz Installing /packages/All/cmake-3.18.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/hdf-szip-2.1.1.txz Installing /packages/All/hdf5-1.10.6,1.txz SUCCEEDED 00:00:27 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.1,1 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.1,1 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.46.1_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by kallisto-0.46.1,1 for building ===> Extracting for kallisto-0.46.1,1 => SHA256 Checksum OK for pachterlab-kallisto-v0.46.1_GH0.tar.gz. Extracted Memory Use: 11.17M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for kallisto-0.46.1,1 ===> Applying ports patches for kallisto-0.46.1,1 from /xports/biology/kallisto/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on package: autoconf>=0 - found ===> kallisto-0.46.1,1 depends on file: /usr/local/bin/cmake - found ===> kallisto-0.46.1,1 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> kallisto-0.46.1,1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> kallisto-0.46.1,1 depends on package: autoconf>=0 - found ===> kallisto-0.46.1,1 depends on file: /usr/local/bin/cmake - found ===> kallisto-0.46.1,1 depends on package: gmake>=4.3 - found ===> kallisto-0.46.1,1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> kallisto-0.46.1,1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> Configuring for kallisto-0.46.1,1 ===> 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 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- 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 USE_HDF5 -- Build files have been written to: /construction/biology/kallisto/.build SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for kallisto-0.46.1,1 gmake[1]: Entering directory '/construction/biology/kallisto/.build' /usr/local/bin/cmake -S/construction/biology/kallisto/kallisto-0.46.1 -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 gmake -f CMakeFiles/Makefile2 all gmake[2]: Entering directory '/construction/biology/kallisto/.build' gmake -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/depend gmake[3]: Entering directory '/construction/biology/kallisto/.build' cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.1 /construction/biology/kallisto/kallisto-0.46.1 /construction/biology/kallisto/.build /construction/biology/kallisto/.build /construction/biology/kallisto/.build/CMakeFiles/htslib.dir/DependInfo.cmake Scanning dependencies of target htslib gmake[3]: Leaving directory '/construction/biology/kallisto/.build' gmake -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/build gmake[3]: Entering directory '/construction/biology/kallisto/.build' [ 3%] Creating directories for 'htslib' /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/tmp /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-mkdir [ 6%] No download step for 'htslib' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-download [ 10%] No update step for 'htslib' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-update [ 13%] No patch step for 'htslib' /usr/local/bin/cmake -E echo_append /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-patch [ 16%] Performing configure step for 'htslib' cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && autoheader && autoconf && /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/configure --prefix= --disable-bz2 --disable-lzma --disable-libcurl checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for ranlib... ranlib checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type... plain .so checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking whether fdatasync is declared... no checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing connect... none required configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-configure [ 20%] Performing build step for 'htslib' cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && gmake lib-static gmake[4]: Entering directory '/construction/biology/kallisto/kallisto-0.46.1/ext/htslib' cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kfunc.o kfunc.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o knetfile.o knetfile.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kstring.o kstring.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bcf_sr_sort.o bcf_sr_sort.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bgzf.o bgzf.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o errmod.o errmod.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o faidx.o faidx.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile.o hfile.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.4.1"' > version.h cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hts.o hts.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o md5.o md5.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o multipart.o multipart.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o probaln.o probaln.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o realn.o realn.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o sam.o sam.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tbx.o tbx.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o textutils.o textutils.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o thread_pool.o thread_pool.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcf.o vcf.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfutils.o vcfutils.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_external.o cram/cram_external.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_index.o cram/cram_index.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_io.o cram/cram_io.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_samtools.o cram/cram_samtools.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/files.o cram/files.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/rANS_static.o cram/rANS_static.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/sam_header.o cram/sam_header.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/vlen.o cram/vlen.c cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/vlen.o cram/zfio.o ranlib libhts.a gmake[4]: Leaving directory '/construction/biology/kallisto/kallisto-0.46.1/ext/htslib' cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-build [ 23%] No install step for 'htslib' cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && /usr/local/bin/cmake -E echo_append cd /construction/biology/kallisto/kallisto-0.46.1/ext/htslib && /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-install [ 26%] Completed 'htslib' /usr/local/bin/cmake -E make_directory /construction/biology/kallisto/.build/CMakeFiles /usr/local/bin/cmake -E touch /construction/biology/kallisto/.build/CMakeFiles/htslib-complete /usr/local/bin/cmake -E touch /construction/biology/kallisto/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-done gmake[3]: Leaving directory '/construction/biology/kallisto/.build' [ 26%] Built target htslib gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend gmake[3]: Entering directory '/construction/biology/kallisto/.build' cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.1 /construction/biology/kallisto/kallisto-0.46.1/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 gmake[3]: Leaving directory '/construction/biology/kallisto/.build' gmake -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build gmake[3]: Entering directory '/construction/biology/kallisto/.build' [ 30%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/BUSData.cpp [ 33%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/BUSTools.cpp [ 36%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/Bootstrap.cpp [ 40%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/GeneModel.cpp [ 43%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/H5Writer.cpp [ 46%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/Kmer.cpp [ 50%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/KmerIndex.cpp [ 53%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/KmerIterator.cpp [ 56%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/Merge.cpp [ 60%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/MinCollector.cpp [ 63%] Building CXX object src/CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/PlaintextWriter.cpp [ 66%] Building CXX object src/CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/ProcessReads.cpp [ 70%] Building CXX object src/CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/PseudoBam.cpp [ 73%] Building CXX object src/CMakeFiles/kallisto_core.dir/common.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/common.cpp [ 76%] Building CXX object src/CMakeFiles/kallisto_core.dir/h5utils.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/h5utils.cpp [ 80%] Building CXX object src/CMakeFiles/kallisto_core.dir/hash.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/hash.cpp [ 83%] Building CXX object src/CMakeFiles/kallisto_core.dir/main.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/main.cpp [ 86%] Building CXX object src/CMakeFiles/kallisto_core.dir/weights.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/src/htslib -I/construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib -I/construction/biology/kallisto/kallisto-0.46.1/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-0.46.1/src/weights.cpp [ 90%] Linking CXX 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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 gmake[3]: Leaving directory '/construction/biology/kallisto/.build' [ 90%] Built target kallisto_core gmake -f src/CMakeFiles/kallisto.dir/build.make src/CMakeFiles/kallisto.dir/depend gmake[3]: Entering directory '/construction/biology/kallisto/.build' cd /construction/biology/kallisto/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/kallisto/kallisto-0.46.1 /construction/biology/kallisto/kallisto-0.46.1/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 gmake[3]: Leaving directory '/construction/biology/kallisto/.build' gmake -f src/CMakeFiles/kallisto.dir/build.make 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/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 /construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib/libhts.a /usr/local/lib/libhdf5.so /usr/local/lib/libsz.so -lz -ldl -lm -lrt gmake[3]: Leaving directory '/construction/biology/kallisto/.build' [100%] Built target kallisto gmake[2]: Leaving directory '/construction/biology/kallisto/.build' /usr/local/bin/cmake -E cmake_progress_start /construction/biology/kallisto/.build/CMakeFiles 0 gmake[1]: Leaving directory '/construction/biology/kallisto/.build' SUCCEEDED 00:04:52 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage 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/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 /construction/biology/kallisto/kallisto-0.46.1/src/../ext/htslib/libhts.a /usr/local/lib/libhdf5.so /usr/local/lib/libsz.so -lz -ldl -lm -lrt gmake[3]: Leaving directory '/construction/biology/kallisto/.build' gmake[2]: Leaving directory '/construction/biology/kallisto/.build' 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 gmake[1]: Leaving directory '/construction/biology/kallisto/.build' install -m 555 /construction/biology/kallisto/kallisto-test /construction/biology/kallisto/stage/usr/local/bin cd /construction/biology/kallisto/kallisto-0.46.1/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 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for kallisto-0.46.1,1 file sizes/checksums [9]: 0% file sizes/checksums [9]: 100% packing files [9]: 0% packing files [9]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:05:31