------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/pciids-20200222.txz Installing /packages/All/libpciaccess-0.16.txz Installing /packages/All/libxml2-2.9.10.txz Installing /packages/All/hwloc-1.11.11.txz Installing /packages/All/libltdl-2.4.6.txz Installing /packages/All/openssl-1.1.1d,1.txz Installing /packages/All/libevent-2.1.11.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.0.2.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/gettext-runtime-0.20.1.txz Installing /packages/All/binutils-2.33.1_2,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openmpi-1.10.7_7.txz Installing /packages/All/libnghttp2-1.40.0.txz Installing /packages/All/ca_root_nss-3.51.txz ===== Message from ca_root_nss-3.51: -- 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/curl-7.68.0.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/jsoncpp-1.9.2.txz Installing /packages/All/libuv-1.35.0.txz Installing /packages/All/rhash-1.3.5.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-3.16.5.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/python37-3.7.6.txz ===== Message from python37-3.7.6: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/perl5-5.30.1.txz ===== Message from perl5-5.30.1: -- The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:01:04 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building ===> Extracting for hhsuite-3.2.0_3 ===> hhsuite-3.2.0_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by hhsuite-3.2.0_3 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.2.0_GH0.tar.gz. Extracted Memory Use: 17.51M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for hhsuite-3.2.0_3 ===> Applying ports patches for hhsuite-3.2.0_3 ===> Applying dragonfly patches for hhsuite-3.2.0_3 /usr/bin/env WRKSRC=/construction/biology/hhsuite/hh-suite-3.2.0 REWARNFILE=/construction/biology/hhsuite/reinplace_warnings.txt /xports/Tools/scripts/sed_checked.sh -e '/find_package(MPI QUIET)/d' -e '/find_package(MPI)/d' /construction/biology/hhsuite/hh-suite-3.2.0/src/CMakeLists.txt /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/CMakeLists.txt /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/mpq/CMakeLists.txt SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on package: openmpi>0 - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/cmake - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/python3.7 - found ===> hhsuite-3.2.0_3 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on package: openmpi>0 - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/cmake - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/python3.7 - found ===> hhsuite-3.2.0_3 depends on package: perl5>=5.30.r1<5.31 - found ===> Configuring for hhsuite-3.2.0_3 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/hhsuite/.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 -- Looking for fmemopen -- Looking for fmemopen - found -- xxd not found, using xxdi.pl instead -- SIMD: HAVE_SSE2 is set -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS MPI MPI_C MPI_CXX Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/hhsuite/.build SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for hhsuite-3.2.0_3 /usr/local/bin/cmake -S/construction/biology/hhsuite/hh-suite-3.2.0 -B/construction/biology/hhsuite/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/hhsuite/.build/CMakeFiles /construction/biology/hhsuite/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- --- data/CMakeFiles/generated.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- --- src/CMakeFiles/A3M_COMPRESS.dir/all --- --- data/CMakeFiles/generated.dir/all --- /usr/bin/make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/depend --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- /usr/bin/make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/depend --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend --- src/CMakeFiles/A3M_COMPRESS.dir/all --- /usr/bin/make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/depend --- data/CMakeFiles/generated.dir/all --- --- data/CMakeFiles/generated.dir/depend --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/depend --- --- data/CMakeFiles/generated.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/data /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/data /construction/biology/hhsuite/.build/data/CMakeFiles/generated.dir/DependInfo.cmake --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src/cs /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src/cs /construction/biology/hhsuite/.build/src/cs/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake --- src/CMakeFiles/A3M_COMPRESS.dir/all --- --- src/CMakeFiles/A3M_COMPRESS.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/A3M_COMPRESS.dir/DependInfo.cmake --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/depend --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- /usr/bin/make -f lib/ffindex/src/mpq/CMakeFiles/mpq.dir/build.make lib/ffindex/src/mpq/CMakeFiles/mpq.dir/depend --- data/CMakeFiles/generated.dir/all --- Scanning dependencies of target generated --- src/CMakeFiles/A3M_COMPRESS.dir/all --- Scanning dependencies of target A3M_COMPRESS --- data/CMakeFiles/generated.dir/all --- /usr/bin/make -f data/CMakeFiles/generated.dir/build.make data/CMakeFiles/generated.dir/build --- src/CMakeFiles/A3M_COMPRESS.dir/all --- /usr/bin/make -f src/CMakeFiles/A3M_COMPRESS.dir/build.make src/CMakeFiles/A3M_COMPRESS.dir/build --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- Scanning dependencies of target CS_OBJECTS --- data/CMakeFiles/generated.dir/all --- --- generated/context_data.crf.h --- --- generated/context_data.lib.h --- --- generated/cs219.lib.h --- --- src/CMakeFiles/A3M_COMPRESS.dir/all --- --- src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/depend --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- /usr/bin/make -f src/cs/CMakeFiles/CS_OBJECTS.dir/build.make src/cs/CMakeFiles/CS_OBJECTS.dir/build --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex.dir/DependInfo.cmake --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- Scanning dependencies of target hhviterbialgorithm_and_ss --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build --- data/CMakeFiles/generated.dir/all --- [ 1%] Generating ../generated/cs219.lib.h --- generated/context_data.crf.h --- [ 1%] Generating ../generated/context_data.crf.h --- generated/context_data.lib.h --- [ 2%] Generating ../generated/context_data.lib.h --- generated/cs219.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mkdir -p /construction/biology/hhsuite/.build/generated --- generated/context_data.crf.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mkdir -p /construction/biology/hhsuite/.build/generated --- generated/context_data.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mkdir -p /construction/biology/hhsuite/.build/generated --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o --- --- data/CMakeFiles/generated.dir/all --- --- generated/cs219.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /construction/biology/hhsuite/hh-suite-3.2.0/cmake/xxdi.pl cs219.lib > /construction/biology/hhsuite/.build/generated/cs219.lib.h --- generated/context_data.crf.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /construction/biology/hhsuite/hh-suite-3.2.0/cmake/xxdi.pl context_data.crf > /construction/biology/hhsuite/.build/generated/context_data.crf.h --- generated/context_data.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /construction/biology/hhsuite/hh-suite-3.2.0/cmake/xxdi.pl context_data.lib > /construction/biology/hhsuite/.build/generated/context_data.lib.h --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- Scanning dependencies of target hhviterbialgorithm_with_celloff /usr/bin/make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- Scanning dependencies of target ffindex --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/depend --- --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex.dir/build.make lib/ffindex/src/CMakeFiles/ffindex.dir/build --- src/CMakeFiles/A3M_COMPRESS.dir/all --- [ 2%] Building CXX object src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_compress.cpp --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/mpq /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src/mpq /construction/biology/hhsuite/.build/lib/ffindex/src/mpq/CMakeFiles/mpq.dir/DependInfo.cmake --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- [ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbialgorithm.cpp --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- [ 3%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex.dir/ffindex.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex.c --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DVITERBI_CELLOFF=1 -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbialgorithm.cpp --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- [ 6%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- [ 6%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- cd /construction/biology/hhsuite/.build/src/cs && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/aa.cc --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbialgorithm.cpp --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- Scanning dependencies of target mpq --- data/CMakeFiles/generated.dir/all --- --- generated/cs219.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /construction/biology/hhsuite/.build/generated/cs219.lib.h > /construction/biology/hhsuite/.build/generated/cs219.lib.h.tmp --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- /usr/bin/make -f lib/ffindex/src/mpq/CMakeFiles/mpq.dir/build.make lib/ffindex/src/mpq/CMakeFiles/mpq.dir/build --- data/CMakeFiles/generated.dir/all --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mv -f /construction/biology/hhsuite/.build/generated/cs219.lib.h.tmp /construction/biology/hhsuite/.build/generated/cs219.lib.h --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o --- --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- [ 6%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o cd /construction/biology/hhsuite/.build/src/cs && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/as.cc --- lib/ffindex/src/mpq/CMakeFiles/mpq.dir/all --- [ 7%] Building C object lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src/mpq && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/mpq.dir/mpq.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/mpq/mpq.c --- lib/ffindex/src/mpq/libmpq.a --- [ 8%] Linking C static library libmpq.a cd /construction/biology/hhsuite/.build/lib/ffindex/src/mpq && /usr/local/bin/cmake -P CMakeFiles/mpq.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/lib/ffindex/src/mpq && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mpq.dir/link.txt --verbose=1 /usr/bin/ar qc libmpq.a CMakeFiles/mpq.dir/mpq.c.o /usr/bin/ranlib libmpq.a [ 8%] Built target mpq --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- --- lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o --- [ 8%] Building C object lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex.dir/ffutil.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffutil.c --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o --- [ 9%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o cd /construction/biology/hhsuite/.build/src/cs && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/assert_helpers.cc --- lib/ffindex/src/CMakeFiles/ffindex.dir/all --- --- lib/ffindex/src/libffindex.a --- [ 10%] Linking C static library libffindex.a cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -P CMakeFiles/ffindex.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex.dir/link.txt --verbose=1 /usr/bin/ar qc libffindex.a CMakeFiles/ffindex.dir/ffindex.c.o CMakeFiles/ffindex.dir/ffutil.c.o /usr/bin/ranlib libffindex.a [ 10%] Built target ffindex --- lib/ffindex/src/CMakeFiles/ffindex_build.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_build.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_build.dir/DependInfo.cmake Scanning dependencies of target ffindex_build /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_build.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_build.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o --- [ 11%] Building C object lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_build.c --- lib/ffindex/src/ffindex_build --- [ 12%] Linking C executable ffindex_build cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_build.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o ffindex_build libffindex.a [ 12%] Built target ffindex_build --- lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/DependInfo.cmake Scanning dependencies of target ffindex_reduce /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o --- [ 12%] Building C object lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_reduce.c --- lib/ffindex/src/ffindex_reduce --- [ 13%] Linking C executable ffindex_reduce cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_reduce.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o ffindex_reduce libffindex.a [ 14%] Built target ffindex_reduce --- lib/ffindex/src/CMakeFiles/ffindex_get.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_get.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_get.dir/DependInfo.cmake Scanning dependencies of target ffindex_get /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_get.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_get.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o --- [ 15%] Building C object lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_get.c --- lib/ffindex/src/ffindex_get --- [ 16%] Linking C executable ffindex_get cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_get.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o ffindex_get libffindex.a [ 16%] Built target ffindex_get --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/DependInfo.cmake Scanning dependencies of target ffindex_from_fasta /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o --- [ 17%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 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-I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/blosum_matrix.cc --- src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o --- [ 19%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o cd /construction/biology/hhsuite/.build/src/cs && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o 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lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_apply.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_apply.dir/DependInfo.cmake Scanning dependencies of target ffindex_apply /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o --- [ 21%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -UHAVE_MPI -o CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c --- lib/ffindex/src/ffindex_apply --- [ 21%] Linking C executable ffindex_apply cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o ffindex_apply libffindex.a [ 22%] Built target ffindex_apply --- lib/ffindex/src/CMakeFiles/ffindex_modify.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_modify.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_modify.dir/DependInfo.cmake Scanning dependencies of target ffindex_modify /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_modify.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o --- [ 23%] Building C object lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_modify.c --- lib/ffindex/src/ffindex_modify --- [ 24%] Linking C executable ffindex_modify cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_modify.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o ffindex_modify libffindex.a --- src/CMakeFiles/hhviterbialgorithm_and_ss.dir/all --- --- src/libhhviterbialgorithm_and_ss.a --- [ 24%] Linking CXX static library libhhviterbialgorithm_and_ss.a cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -P CMakeFiles/hhviterbialgorithm_and_ss.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_and_ss.a CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_and_ss.a [ 24%] Built target hhviterbialgorithm_and_ss --- lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/DependInfo.cmake Scanning dependencies of target ffindex_apply_mpi /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o --- [ 25%] Building C object lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DHAVE_MPI=1 -I/usr/local/mpi/openmpi/include -o CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_apply_mpi.c --- lib/ffindex/src/ffindex_apply_mpi --- [ 25%] Linking C executable ffindex_apply_mpi cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_apply_mpi.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -o ffindex_apply_mpi libffindex.a mpq/libmpq.a [ 26%] Built target ffindex_apply_mpi --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/DependInfo.cmake Scanning dependencies of target ffindex_from_fasta_with_split /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o --- [ 27%] Building C object lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_from_fasta_with_split.c --- lib/ffindex/src/ffindex_from_fasta_with_split --- [ 28%] Linking C executable ffindex_from_fasta_with_split cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_from_fasta_with_split.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o ffindex_from_fasta_with_split libffindex.a [ 28%] Built target ffindex_from_fasta_with_split --- lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/DependInfo.cmake Scanning dependencies of target ffindex_unpack /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o --- [ 28%] Building C object lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_unpack.c --- lib/ffindex/src/ffindex_unpack --- [ 29%] Linking C executable ffindex_unpack cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_unpack.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o ffindex_unpack libffindex.a [ 30%] Built target ffindex_unpack --- lib/ffindex/src/CMakeFiles/ffindex_order.dir/all --- /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend --- lib/ffindex/src/CMakeFiles/ffindex_order.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/lib/ffindex/src /construction/biology/hhsuite/.build/lib/ffindex/src/CMakeFiles/ffindex_order.dir/DependInfo.cmake Scanning dependencies of target ffindex_order /usr/bin/make -f lib/ffindex/src/CMakeFiles/ffindex_order.dir/build.make lib/ffindex/src/CMakeFiles/ffindex_order.dir/build --- lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o --- [ 30%] Building C object lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/bin/cc -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ext -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src/ffindex_order.c --- lib/ffindex/src/CMakeFiles/ffindex_modify.dir/all --- [ 31%] Built target ffindex_modify --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o --- [ 32%] Building CXX object src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o cd /construction/biology/hhsuite/.build/src/cs && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/application.cc --- lib/ffindex/src/CMakeFiles/ffindex_order.dir/all --- --- lib/ffindex/src/ffindex_order --- [ 33%] Linking C executable ffindex_order cd /construction/biology/hhsuite/.build/lib/ffindex/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ffindex_order.dir/link.txt --verbose=1 /usr/bin/cc -std=c99 -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o ffindex_order libffindex.a [ 34%] Built target ffindex_order --- src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/all --- --- src/libhhviterbialgorithm_with_celloff.a --- [ 35%] Linking CXX static library libhhviterbialgorithm_with_celloff.a cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff.a CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff.a [ 35%] Built target hhviterbialgorithm_with_celloff --- src/CMakeFiles/A3M_COMPRESS.dir/all --- --- src/libA3M_COMPRESS.a --- [ 36%] Linking CXX static library libA3M_COMPRESS.a cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -P CMakeFiles/A3M_COMPRESS.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/A3M_COMPRESS.dir/link.txt --verbose=1 /usr/bin/ar qc libA3M_COMPRESS.a CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o /usr/bin/ranlib libA3M_COMPRESS.a [ 36%] Built target A3M_COMPRESS --- src/CMakeFiles/a3m_database_extract.dir/all --- --- src/CMakeFiles/a3m_reduce.dir/all --- --- src/CMakeFiles/a3m_extract.dir/all --- --- src/CMakeFiles/a3m_database_reduce.dir/all --- --- src/CMakeFiles/a3m_database_filter.dir/all --- --- src/CMakeFiles/a3m_database_extract.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend --- src/CMakeFiles/a3m_reduce.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend --- src/CMakeFiles/a3m_extract.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend --- src/CMakeFiles/a3m_database_reduce.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend --- src/CMakeFiles/a3m_database_filter.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend --- src/CMakeFiles/a3m_database_extract.dir/all --- --- src/CMakeFiles/a3m_database_extract.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake --- src/CMakeFiles/a3m_reduce.dir/all --- --- src/CMakeFiles/a3m_reduce.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake --- src/CMakeFiles/a3m_database_reduce.dir/all --- --- src/CMakeFiles/a3m_database_reduce.dir/depend --- --- src/CMakeFiles/a3m_database_filter.dir/all --- --- src/CMakeFiles/a3m_database_filter.dir/depend --- --- src/CMakeFiles/a3m_database_extract.dir/all --- Scanning dependencies of target a3m_database_extract --- src/CMakeFiles/a3m_database_filter.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake --- src/CMakeFiles/a3m_database_extract.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build --- src/CMakeFiles/a3m_reduce.dir/all --- Scanning dependencies of target a3m_reduce --- src/CMakeFiles/a3m_database_reduce.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake --- src/CMakeFiles/a3m_extract.dir/all --- --- src/CMakeFiles/a3m_extract.dir/depend --- --- src/CMakeFiles/a3m_reduce.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build --- src/CMakeFiles/a3m_extract.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake --- src/CMakeFiles/a3m_database_extract.dir/all --- --- src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o --- --- src/CMakeFiles/a3m_database_reduce.dir/all --- Scanning dependencies of target a3m_database_reduce --- src/CMakeFiles/a3m_extract.dir/all --- Scanning dependencies of target a3m_extract --- src/CMakeFiles/a3m_database_reduce.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build --- src/CMakeFiles/a3m_extract.dir/all --- /usr/bin/make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build --- src/CMakeFiles/a3m_database_extract.dir/all --- [ 37%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_database_extract.cpp --- src/CMakeFiles/a3m_reduce.dir/all --- --- src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o --- --- src/CMakeFiles/a3m_database_reduce.dir/all --- --- src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o --- --- src/CMakeFiles/a3m_extract.dir/all --- --- src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o --- --- src/CMakeFiles/a3m_reduce.dir/all --- [ 37%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_reduce.cpp --- src/CMakeFiles/a3m_extract.dir/all --- [ 37%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o --- src/CMakeFiles/a3m_database_reduce.dir/all --- [ 38%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o --- src/CMakeFiles/a3m_extract.dir/all --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_extract.cpp --- src/CMakeFiles/a3m_database_reduce.dir/all --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_database_reduce.cpp --- src/CMakeFiles/a3m_database_filter.dir/all --- Scanning dependencies of target a3m_database_filter /usr/bin/make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build --- src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o --- [ 39%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/a3m_database_filter.cpp --- src/CMakeFiles/a3m_database_extract.dir/all --- --- src/a3m_database_extract --- [ 40%] Linking CXX executable a3m_database_extract cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o a3m_database_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 40%] Built target a3m_database_extract --- src/CMakeFiles/a3m_reduce.dir/all --- --- src/a3m_reduce --- [ 41%] Linking CXX executable a3m_reduce cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o a3m_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 42%] Built target a3m_reduce --- src/CMakeFiles/a3m_database_reduce.dir/all --- --- src/a3m_database_reduce --- [ 43%] Linking CXX executable a3m_database_reduce cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o a3m_database_reduce ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 44%] Built target a3m_database_reduce --- src/CMakeFiles/a3m_extract.dir/all --- --- src/a3m_extract --- [ 45%] Linking CXX executable a3m_extract cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o a3m_extract ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a [ 46%] Built target a3m_extract --- src/CMakeFiles/a3m_database_filter.dir/all --- --- src/a3m_database_filter --- [ 47%] Linking CXX executable a3m_database_filter cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_filter.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o a3m_database_filter ../lib/ffindex/src/libffindex.a libA3M_COMPRESS.a --- src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/all --- --- src/libhhviterbialgorithm_with_celloff_and_ss.a --- [ 48%] Linking CXX static library libhhviterbialgorithm_with_celloff_and_ss.a cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -P CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/link.txt --verbose=1 /usr/bin/ar qc libhhviterbialgorithm_with_celloff_and_ss.a CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/ranlib libhhviterbialgorithm_with_celloff_and_ss.a [ 48%] Built target hhviterbialgorithm_with_celloff_and_ss --- src/CMakeFiles/a3m_database_filter.dir/all --- [ 48%] Built target a3m_database_filter --- data/CMakeFiles/generated.dir/all --- --- generated/context_data.lib.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /construction/biology/hhsuite/.build/generated/context_data.lib.h > /construction/biology/hhsuite/.build/generated/context_data.lib.h.tmp cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mv -f /construction/biology/hhsuite/.build/generated/context_data.lib.h.tmp /construction/biology/hhsuite/.build/generated/context_data.lib.h --- src/cs/CMakeFiles/CS_OBJECTS.dir/all --- --- src/cs/libCS_OBJECTS.a --- [ 48%] Linking CXX static library libCS_OBJECTS.a cd /construction/biology/hhsuite/.build/src/cs && /usr/local/bin/cmake -P CMakeFiles/CS_OBJECTS.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src/cs && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/CS_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libCS_OBJECTS.a CMakeFiles/CS_OBJECTS.dir/aa.cc.o CMakeFiles/CS_OBJECTS.dir/as.cc.o CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/log.cc.o CMakeFiles/CS_OBJECTS.dir/application.cc.o /usr/bin/ranlib libCS_OBJECTS.a [ 48%] Built target CS_OBJECTS --- data/CMakeFiles/generated.dir/all --- --- generated/context_data.crf.h --- cd /construction/biology/hhsuite/hh-suite-3.2.0/data && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /construction/biology/hhsuite/.build/generated/context_data.crf.h > /construction/biology/hhsuite/.build/generated/context_data.crf.h.tmp cd /construction/biology/hhsuite/hh-suite-3.2.0/data && mv -f /construction/biology/hhsuite/.build/generated/context_data.crf.h.tmp /construction/biology/hhsuite/.build/generated/context_data.crf.h [ 48%] Built target generated --- src/CMakeFiles/HH_OBJECTS.dir/all --- /usr/bin/make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend --- src/CMakeFiles/HH_OBJECTS.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake Scanning dependencies of target HH_OBJECTS /usr/bin/make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build --- src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o --- --- src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o --- [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhsearch.cpp --- src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o --- [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o --- src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o --- [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o --- src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/util.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhhitlist.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o --- [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhposteriordecoder.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o --- [ 51%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhutil.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o --- [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhalign.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o --- [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhblits.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o --- [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhmatrices.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o --- [ 54%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhdecl.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o --- [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhhit.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o --- [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhalignment.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o --- [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhforwardalgorithm.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o --- [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhhmm.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o --- [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhposteriordecoderrunner.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o --- [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbialgorithm.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o --- [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhfullalignment.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o --- [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhhmmsimd.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o --- [ 61%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhposteriormatrix.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o --- [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbi.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o --- [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhbacktracemac.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o --- [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhmacalgorithm.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o --- [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhprefilter.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o --- [ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbimatrix.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o --- [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhbackwardalgorithm.cpp --- src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o --- [ 66%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/ffindexdatabase.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o --- [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhdatabase.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o --- [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhhalfalignment.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o --- [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhviterbirunner.cpp --- src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o --- [ 69%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhfunc.cpp --- src/libHH_OBJECTS.a --- [ 69%] Linking CXX static library libHH_OBJECTS.a cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -P CMakeFiles/HH_OBJECTS.dir/cmake_clean_target.cmake cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/HH_OBJECTS.dir/link.txt --verbose=1 /usr/bin/ar qc libHH_OBJECTS.a CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/ffindexdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o /usr/bin/ranlib libHH_OBJECTS.a [ 69%] Built target HH_OBJECTS --- src/CMakeFiles/cstranslate_mpi.dir/all --- --- src/CMakeFiles/hhalign_mpi.dir/all --- --- src/CMakeFiles/hhsearch_mpi.dir/all --- --- src/CMakeFiles/hhblits_mpi.dir/all --- --- src/CMakeFiles/hhblits_ca3m.dir/all --- --- src/CMakeFiles/hhalign_omp.dir/all --- --- src/CMakeFiles/hhsearch_omp.dir/all --- --- src/CMakeFiles/hhblits_omp.dir/all --- --- src/CMakeFiles/cstranslate.dir/all --- --- src/CMakeFiles/hhsearch.dir/all --- --- src/CMakeFiles/cstranslate_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/cstranslate_mpi.dir/build.make src/CMakeFiles/cstranslate_mpi.dir/depend --- src/CMakeFiles/hhalign_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhalign_mpi.dir/build.make src/CMakeFiles/hhalign_mpi.dir/depend --- src/CMakeFiles/hhblits_ca3m.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/depend --- src/CMakeFiles/hhsearch_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/depend --- src/CMakeFiles/hhblits_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/depend --- src/CMakeFiles/hhsearch_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhsearch_mpi.dir/build.make src/CMakeFiles/hhsearch_mpi.dir/depend --- src/CMakeFiles/hhblits_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_mpi.dir/build.make src/CMakeFiles/hhblits_mpi.dir/depend --- src/CMakeFiles/hhalign_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/depend --- src/CMakeFiles/cstranslate.dir/all --- /usr/bin/make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend --- src/CMakeFiles/hhsearch.dir/all --- /usr/bin/make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend --- src/CMakeFiles/hhsearch_omp.dir/all --- --- src/CMakeFiles/hhsearch_omp.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhsearch_omp.dir/DependInfo.cmake --- src/CMakeFiles/hhblits_omp.dir/all --- --- src/CMakeFiles/hhblits_omp.dir/depend --- --- src/CMakeFiles/hhblits_mpi.dir/all --- --- src/CMakeFiles/hhblits_mpi.dir/depend --- --- src/CMakeFiles/hhblits_omp.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhblits_omp.dir/DependInfo.cmake --- src/CMakeFiles/hhalign_mpi.dir/all --- --- src/CMakeFiles/hhalign_mpi.dir/depend --- --- src/CMakeFiles/hhblits_mpi.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhblits_mpi.dir/DependInfo.cmake --- src/CMakeFiles/hhalign_mpi.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhalign_mpi.dir/DependInfo.cmake --- src/CMakeFiles/hhalign_omp.dir/all --- --- src/CMakeFiles/hhalign_omp.dir/depend --- --- src/CMakeFiles/hhsearch.dir/all --- --- src/CMakeFiles/hhsearch.dir/depend --- --- src/CMakeFiles/cstranslate_mpi.dir/all --- --- src/CMakeFiles/cstranslate_mpi.dir/depend --- --- src/CMakeFiles/hhalign_omp.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhalign_omp.dir/DependInfo.cmake --- src/CMakeFiles/hhsearch.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhsearch.dir/DependInfo.cmake --- src/CMakeFiles/cstranslate.dir/all --- --- src/CMakeFiles/cstranslate.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/cstranslate.dir/DependInfo.cmake --- src/CMakeFiles/hhsearch_mpi.dir/all --- --- src/CMakeFiles/hhsearch_mpi.dir/depend --- --- src/CMakeFiles/cstranslate_mpi.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/cstranslate_mpi.dir/DependInfo.cmake --- src/CMakeFiles/hhsearch_mpi.dir/all --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhsearch_mpi.dir/DependInfo.cmake --- src/CMakeFiles/hhblits_ca3m.dir/all --- --- src/CMakeFiles/hhblits_ca3m.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhblits_ca3m.dir/DependInfo.cmake --- src/CMakeFiles/hhsearch_omp.dir/all --- Scanning dependencies of target hhsearch_omp --- src/CMakeFiles/hhblits_omp.dir/all --- Scanning dependencies of target hhblits_omp --- src/CMakeFiles/hhsearch_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhsearch_omp.dir/build.make src/CMakeFiles/hhsearch_omp.dir/build --- src/CMakeFiles/hhblits_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_omp.dir/build.make src/CMakeFiles/hhblits_omp.dir/build --- src/CMakeFiles/hhsearch.dir/all --- Scanning dependencies of target hhsearch /usr/bin/make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build --- src/CMakeFiles/hhsearch_omp.dir/all --- --- src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o --- --- src/CMakeFiles/hhblits_omp.dir/all --- --- src/CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o --- --- src/CMakeFiles/hhblits_mpi.dir/all --- Scanning dependencies of target hhblits_mpi --- src/CMakeFiles/hhalign_mpi.dir/all --- Scanning dependencies of target hhalign_mpi --- src/CMakeFiles/hhblits_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_mpi.dir/build.make src/CMakeFiles/hhblits_mpi.dir/build --- src/CMakeFiles/hhalign_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhalign_mpi.dir/build.make src/CMakeFiles/hhalign_mpi.dir/build --- src/CMakeFiles/hhalign_omp.dir/all --- Scanning dependencies of target hhalign_omp --- src/CMakeFiles/hhsearch_omp.dir/all --- [ 70%] Building CXX object src/CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o --- src/CMakeFiles/hhalign_omp.dir/all --- /usr/bin/make -f src/CMakeFiles/hhalign_omp.dir/build.make src/CMakeFiles/hhalign_omp.dir/build --- src/CMakeFiles/hhsearch_omp.dir/all --- cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DHHSEARCH=1 -o 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-I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhblits_omp.cpp --- src/CMakeFiles/hhsearch_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/hhsearch_mpi.dir/build.make src/CMakeFiles/hhsearch_mpi.dir/build --- src/CMakeFiles/hhblits_ca3m.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits_ca3m.dir/build.make src/CMakeFiles/hhblits_ca3m.dir/build --- src/CMakeFiles/hhblits_mpi.dir/all --- [ 72%] Building CXX object src/CMakeFiles/hhblits_mpi.dir/hhblits_mpi.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated 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-I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -DHHSEARCH=1 -o CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhblits_app.cpp --- src/CMakeFiles/cstranslate.dir/all --- Scanning dependencies of target cstranslate /usr/bin/make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build --- src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o --- --- src/CMakeFiles/cstranslate_mpi.dir/all --- Scanning dependencies of target cstranslate_mpi --- src/CMakeFiles/cstranslate.dir/all --- [ 75%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/cstranslate_app.cc --- src/CMakeFiles/cstranslate_mpi.dir/all --- /usr/bin/make -f src/CMakeFiles/cstranslate_mpi.dir/build.make src/CMakeFiles/cstranslate_mpi.dir/build --- src/CMakeFiles/cstranslate_mpi.dir/cs/cstranslate_mpi_app.cc.o --- [ 75%] Building CXX object src/CMakeFiles/cstranslate_mpi.dir/cs/cstranslate_mpi_app.cc.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -I/usr/local/mpi/openmpi/include -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -I/usr/local/mpi/openmpi/include -o CMakeFiles/cstranslate_mpi.dir/cs/cstranslate_mpi_app.cc.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/cs/cstranslate_mpi_app.cc --- src/CMakeFiles/hhsearch.dir/all --- --- src/hhsearch --- [ 76%] Linking CXX executable hhsearch cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/hhsearch.dir/hhblits_app.cpp.o -o hhsearch libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 77%] Built target hhsearch --- src/CMakeFiles/hhalign.dir/all --- /usr/bin/make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend --- src/CMakeFiles/hhalign.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhalign.dir/DependInfo.cmake Scanning dependencies of target hhalign /usr/bin/make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build --- src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o --- [ 78%] Building CXX object src/CMakeFiles/hhalign.dir/hhblits_app.cpp.o cd 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-L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/hhblits_ca3m.dir/hhblits_ca3m.cpp.o -o hhblits_ca3m libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 79%] Built target hhblits_ca3m --- src/CMakeFiles/hhblits.dir/all --- /usr/bin/make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend --- src/CMakeFiles/hhblits.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhblits.dir/DependInfo.cmake Scanning dependencies of target hhblits /usr/bin/make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build --- src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o --- [ 80%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhblits_app.cpp --- src/CMakeFiles/hhsearch_omp.dir/all --- --- src/hhsearch_omp --- [ 80%] Linking CXX executable hhsearch_omp cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhsearch_omp.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/hhsearch_omp.dir/hhblits_omp.cpp.o -o hhsearch_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 81%] Built target hhsearch_omp --- src/CMakeFiles/hhmake.dir/all --- /usr/bin/make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend --- src/CMakeFiles/hhmake.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhmake.dir/DependInfo.cmake Scanning dependencies of target hhmake /usr/bin/make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build --- src/CMakeFiles/hhmake.dir/hhmake.cpp.o --- [ 81%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhmake.cpp --- src/CMakeFiles/hhblits_omp.dir/all --- --- src/hhblits_omp --- [ 82%] Linking CXX executable hhblits_omp cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/hhblits_omp.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi CMakeFiles/hhblits_omp.dir/hhblits_omp.cpp.o -o hhblits_omp libHH_OBJECTS.a ../lib/ffindex/src/libffindex.a cs/libCS_OBJECTS.a libhhviterbialgorithm_with_celloff.a libhhviterbialgorithm_and_ss.a libhhviterbialgorithm_with_celloff_and_ss.a [ 82%] Built target hhblits_omp --- src/CMakeFiles/hhfilter.dir/all --- /usr/bin/make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend --- src/CMakeFiles/hhfilter.dir/depend --- cd /construction/biology/hhsuite/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/hhsuite/hh-suite-3.2.0 /construction/biology/hhsuite/hh-suite-3.2.0/src /construction/biology/hhsuite/.build /construction/biology/hhsuite/.build/src /construction/biology/hhsuite/.build/src/CMakeFiles/hhfilter.dir/DependInfo.cmake Scanning dependencies of target hhfilter /usr/bin/make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build --- src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o --- [ 82%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o cd /construction/biology/hhsuite/.build/src && /usr/bin/c++ -DOPENMP -DSSE -I/construction/biology/hhsuite/.build/generated -I/construction/biology/hhsuite/hh-suite-3.2.0/src -I/construction/biology/hhsuite/hh-suite-3.2.0/lib/ffindex/src -I/construction/biology/hhsuite/.build/src -I/construction/biology/hhsuite/hh-suite-3.2.0/src/cs -pipe -O2 -fno-strict-aliasing -std=c++0x -msse -msse2 -fopenmp -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c /construction/biology/hhsuite/hh-suite-3.2.0/src/hhfilter.cpp --- src/CMakeFiles/hhalign_mpi.dir/all --- --- src/hhalign_mpi --- [ 82%] Linking CXX executable hhalign_mpi cd /construction/biology/hhsuite/.build/src && /usr/local/bin/cmake -E cmake_link_script 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------------------------------------------------------------------------------- ===> hhsuite-3.2.0_3 depends on package: openmpi>0 - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/python3.7 - found ===> hhsuite-3.2.0_3 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for hhsuite-3.2.0_3 ===> hhsuite-3.2.0_3 depends on package: openmpi>0 - found ===> hhsuite-3.2.0_3 depends on file: /usr/local/bin/python3.7 - found ===> hhsuite-3.2.0_3 depends on package: perl5>=5.30.r1<5.31 - found ===> Generating temporary packing list /usr/local/bin/cmake -S/construction/biology/hhsuite/hh-suite-3.2.0 -B/construction/biology/hhsuite/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/hhsuite/.build/CMakeFiles 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