=> Building biology/kallisto Started : Sunday, 7 JUL 2019 at 04:20:12 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for kallisto-0.46.0: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/kallisto XDG_CONFIG_HOME=/construction/biology/kallisto HOME=/construction/biology/kallisto TMPDIR="/tmp" PATH=/construction/biology/kallisto/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/kallisto XDG_CONFIG_HOME=/construction/biology/kallisto HOME=/construction/biology/kallisto TMPDIR="/tmp" PATH=/construction/biology/kallisto/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/kallisto/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> kallisto-0.46.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> kallisto-0.46.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.46.0 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.46.0 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.46.0 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.46.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.46.0 for building ===> Extracting for kallisto-0.46.0 => SHA256 Checksum OK for pachterlab-kallisto-v0.46.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for kallisto-0.46.0 ===> Applying ports patches for kallisto-0.46.0 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> kallisto-0.46.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.14.5.txz Installing cmake-3.14.5... `-- Installing curl-7.65.1... | `-- Installing ca_root_nss-3.44... | `-- Extracting ca_root_nss-3.44: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done `-- Extracting curl-7.65.1: .......... done `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing jsoncpp-1.8.1_6... `-- Extracting jsoncpp-1.8.1_6: .......... done `-- Installing libarchive-3.3.3,1... | `-- Installing liblz4-1.9.1,1... | `-- Extracting liblz4-1.9.1,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.3,1: .......... done `-- Installing libuv-1.29.1... `-- Extracting libuv-1.29.1: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.14.5: .......... done Message from ca_root_nss-3.44: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> kallisto-0.46.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of kallisto-0.46.0 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> kallisto-0.46.0 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.5_1.txz Installing hdf5-1.10.5_1... `-- Installing hdf-szip-2.1.1... `-- Extracting hdf-szip-2.1.1: .......... done Extracting hdf5-1.10.5_1: .......... done ===> kallisto-0.46.0 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of kallisto-0.46.0 ===> kallisto-0.46.0 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> kallisto-0.46.0 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz Installing htslib-1.9... Extracting htslib-1.9: .......... done ===> kallisto-0.46.0 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of kallisto-0.46.0 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for kallisto-0.46.0 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/kallisto/.build -- The C compiler identification is GNU 8.1.0 -- The CXX compiler identification is GNU 8.1.0 -- 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 "1.10.5") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for kallisto-0.46.0 /usr/local/bin/cmake -S/construction/biology/kallisto/kallisto-0.46.0 -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-0.46.0 /construction/biology/kallisto/kallisto-0.46.0/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/Bootstrap.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o --- src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o --- src/CMakeFiles/kallisto_core.dir/GeneModel.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/GeneModel.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/GeneModel.cpp --- src/CMakeFiles/kallisto_core.dir/H5Writer.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/H5Writer.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/H5Writer.cpp --- src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o --- cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/Bootstrap.cpp --- src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/BUSData.cpp --- src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/BUSTools.cpp --- src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o --- [ 27%] Building CXX object src/CMakeFiles/kallisto_core.dir/Kmer.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/Kmer.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/Kmer.cpp --- src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o --- [ 31%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIndex.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/KmerIndex.cpp --- src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o --- [ 36%] Building CXX object src/CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/KmerIterator.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/KmerIterator.cpp --- src/CMakeFiles/kallisto_core.dir/Merge.cpp.o --- [ 40%] Building CXX object src/CMakeFiles/kallisto_core.dir/Merge.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/Merge.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/Merge.cpp --- src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o --- [ 45%] Building CXX object src/CMakeFiles/kallisto_core.dir/MinCollector.cpp.o cd /construction/biology/kallisto/.build/src && /usr/bin/c++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/MinCollector.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/src/MinCollector.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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/PlaintextWriter.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/ProcessReads.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/PseudoBam.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/common.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/h5utils.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/hash.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/main.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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++ -I/construction/biology/kallisto/kallisto-0.46.0/src -I/usr/local/include -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto_core.dir/weights.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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-0.46.0 /construction/biology/kallisto/kallisto-0.46.0/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++ -I/usr/local/include -I/construction/biology/kallisto/kallisto-0.46.0/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -std=c++11 -o CMakeFiles/kallisto.dir/main.cpp.o -c /construction/biology/kallisto/kallisto-0.46.0/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 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -L/usr/local/lib CMakeFiles/kallisto.dir/main.cpp.o -o kallisto -Wl,-z,origin,-rpath,/usr/local/lib libkallisto_core.a -lpthread -lhts /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 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for kallisto-0.46.0 ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/kallisto/kallisto-0.46.0 -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-0.46.0 /construction/biology/kallisto/kallisto-0.46.0/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-0.46.0 /construction/biology/kallisto/kallisto-0.46.0/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 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -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 /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-0.46.0/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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for kallisto-0.46.0 file sizes/checksums [12]: . done packing files [12]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:21:03 UTC Duration: 00:00:51