------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for abyss-2.3.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/abyss XDG_CONFIG_HOME=/construction/biology/abyss HOME=/construction/biology/abyss TMPDIR="/tmp" PATH=/construction/biology/abyss/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/abyss XDG_CONFIG_HOME=/construction/biology/abyss HOME=/construction/biology/abyss TMPDIR="/tmp" PATH=/construction/biology/abyss/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/abyss/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=24 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/icu-69.1,1.txz Installing /packages/All/boost-libs-1.72.0_5.txz ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < use databases/sqlite3@default Installing /packages/All/tcl86-8.6.11_1.txz Installing /packages/All/libedit-3.1.20210216,1.txz Installing /packages/All/sqlite3-3.35.5_3,1.txz Installing /packages/All/readline-8.1.1.txz Installing /packages/All/bash-5.1.8.txz UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default SUCCEEDED 00:00:24 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by abyss-2.3.1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by abyss-2.3.1 for building => SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by abyss-2.3.1 for building ===> Extracting for abyss-2.3.1 => SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz. Extracted Memory Use: 8.50M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for abyss-2.3.1 ===> Applying ports patches for abyss-2.3.1 from /xports/biology/abyss/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - found ===> abyss-2.3.1 depends on executable: ghc - found ===> abyss-2.3.1 depends on executable: pandoc - found ===> abyss-2.3.1 depends on package: gmake>=4.3 - found ===> abyss-2.3.1 depends on package: autoconf>=2.69 - found ===> abyss-2.3.1 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on shared library: libffi.so - found (/usr/local/lib/libffi.so) ===> abyss-2.3.1 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> abyss-2.3.1 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) ===> abyss-2.3.1 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - found ===> abyss-2.3.1 depends on executable: ghc - found ===> abyss-2.3.1 depends on executable: pandoc - found ===> abyss-2.3.1 depends on package: gmake>=4.3 - found ===> abyss-2.3.1 depends on package: autoconf>=2.69 - found ===> abyss-2.3.1 depends on package: automake>=1.16.1 - found ===> abyss-2.3.1 depends on shared library: libffi.so - found (/usr/local/lib/libffi.so) ===> abyss-2.3.1 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> abyss-2.3.1 depends on shared library: libiconv.so - found (/usr/local/lib/libiconv.so) ===> abyss-2.3.1 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so) ===> Configuring for abyss-2.3.1 configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:167: installing './config.guess' configure.ac:167: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' configure: loading site script /xports/Templates/config.site checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking whether c++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports the include directive... yes (GNU style) checking whether gmake supports nested variables... yes checking dependency style of c++ -std=c++11... gcc3 checking for gawk... (cached) /usr/bin/awk checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking whether we are using the GNU C++ compiler... (cached) yes checking whether c++ -std=c++11 accepts -g... (cached) yes checking for ranlib... ranlib checking for ghc... ghc The Glorious Glasgow Haskell Compilation System, version 8.10.5 checking for pandoc... yes checking for ar... ar checking the archiver (ar) interface... ar checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for fcntl.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stddef.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... (cached) yes checking for mode_t... (cached) yes checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for int64_t... (cached) yes checking for uint8_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint64_t... (cached) yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... (cached) yes checking for gethostname... (cached) yes checking for getopt_long... yes checking for getpagesize... (cached) yes checking for memset... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strtoul... (cached) yes checking for vfork.h... (cached) no checking for fork... (cached) yes checking for vfork... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... (cached) yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... no checking build system type... x86_64-portbld-dragonfly6.1 checking host system type... x86_64-portbld-dragonfly6.1 checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no checking for MPI_Init in -lmpi... no checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... c++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... no checking google/sparse_hash_map presence... no checking for google/sparse_hash_map... no checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for c++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands SUCCEEDED 00:00:20 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for abyss-2.3.1 gmake[1]: Entering directory '/construction/biology/abyss/abyss-2.3.1' gmake all-recursive gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1' Making all in bin gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/bin' cp ../bin/abyss-nompi ABYSS-P gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/bin' Making all in doc gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/doc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/doc' Making all in Common gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Common' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-ContigID.o -MD -MP -MF .deps/libcommon_a-ContigID.Tpo -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Fcontrol.o -MD -MP -MF .deps/libcommon_a-Fcontrol.Tpo -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Histogram.o -MD -MP -MF .deps/libcommon_a-Histogram.Tpo -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Kmer.o -MD -MP -MF .deps/libcommon_a-Kmer.Tpo -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Log.o -MD -MP -MF .deps/libcommon_a-Log.Tpo -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Options.o -MD -MP -MF .deps/libcommon_a-Options.Tpo -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Sequence.o -MD -MP -MF .deps/libcommon_a-Sequence.Tpo -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-SignalHandler.o -MD -MP -MF .deps/libcommon_a-SignalHandler.Tpo -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Timer.o -MD -MP -MF .deps/libcommon_a-Timer.Tpo -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-Uncompress.o -MD -MP -MF .deps/libcommon_a-Uncompress.Tpo -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libcommon_a-city.o -MD -MP -MF .deps/libcommon_a-city.Tpo -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc mv -f .deps/libcommon_a-Options.Tpo .deps/libcommon_a-Options.Po mv -f .deps/libcommon_a-Fcontrol.Tpo .deps/libcommon_a-Fcontrol.Po mv -f .deps/libcommon_a-city.Tpo .deps/libcommon_a-city.Po mv -f .deps/libcommon_a-Timer.Tpo .deps/libcommon_a-Timer.Po mv -f .deps/libcommon_a-Log.Tpo .deps/libcommon_a-Log.Po mv -f .deps/libcommon_a-SignalHandler.Tpo .deps/libcommon_a-SignalHandler.Po mv -f .deps/libcommon_a-Kmer.Tpo .deps/libcommon_a-Kmer.Po mv -f .deps/libcommon_a-Sequence.Tpo .deps/libcommon_a-Sequence.Po mv -f .deps/libcommon_a-ContigID.Tpo .deps/libcommon_a-ContigID.Po mv -f .deps/libcommon_a-Uncompress.Tpo .deps/libcommon_a-Uncompress.Po mv -f .deps/libcommon_a-Histogram.Tpo .deps/libcommon_a-Histogram.Po rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Common' Making all in Graph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Graph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gc-gc.o -MD -MP -MF .deps/abyss_gc-gc.Tpo -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_todot-todot.o -MD -MP -MF .deps/abyss_todot-todot.Tpo -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc mv -f .deps/abyss_gc-gc.Tpo .deps/abyss_gc-gc.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_todot-todot.Tpo .deps/abyss_todot-todot.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L. -L/usr/local/lib -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Graph' Making all in DataLayer gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fac-fac.o -MD -MP -MF .deps/abyss_fac-fac.Tpo -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaReader.o -MD -MP -MF .deps/libdatalayer_a-FastaReader.Tpo -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdatalayer_a-FastaWriter.o -MD -MP -MF .deps/libdatalayer_a-FastaWriter.Tpo -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_tofastq-abyss-tofastq.o -MD -MP -MF .deps/abyss_tofastq-abyss-tofastq.Tpo -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc mv -f .deps/libdatalayer_a-FastaWriter.Tpo .deps/libdatalayer_a-FastaWriter.Po mv -f .deps/abyss_tofastq-abyss-tofastq.Tpo .deps/abyss_tofastq-abyss-tofastq.Po mv -f .deps/abyss_fac-fac.Tpo .deps/abyss_fac-fac.Po mv -f .deps/libdatalayer_a-FastaReader.Tpo .deps/libdatalayer_a-FastaReader.Po rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' Making all in DataBase gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataBase' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-DB.o -MD -MP -MF .deps/abyss_db_csv-DB.Tpo -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_db_csv-db-csv.o -MD -MP -MF .deps/abyss_db_csv-db-csv.Tpo -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libdb_a-DB.o -MD -MP -MF .deps/libdb_a-DB.Tpo -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc mv -f .deps/abyss_db_csv-db-csv.Tpo .deps/abyss_db_csv-db-csv.Po mv -f .deps/abyss_db_csv-DB.Tpo .deps/abyss_db_csv-DB.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm mv -f .deps/libdb_a-DB.Tpo .deps/libdb_a-DB.Po rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataBase' Making all in FMIndex gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_count-count.o -MD -MP -MF .deps/abyss_count-count.Tpo -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libfmindex_a-bit_array.o -MD -MP -MF .deps/libfmindex_a-bit_array.Tpo -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_dawg-abyss-dawg.o -MD -MP -MF .deps/abyss_dawg-abyss-dawg.Tpo -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc mv -f .deps/libfmindex_a-bit_array.Tpo .deps/libfmindex_a-bit_array.Po rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a mv -f .deps/abyss_count-count.Tpo .deps/abyss_count-count.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_dawg-abyss-dawg.Tpo .deps/abyss_dawg-abyss-dawg.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' Making all in Assembly gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Assembly' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-AssemblyAlgorithms.o -MD -MP -MF .deps/libassembly_a-AssemblyAlgorithms.Tpo -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libassembly_a-Options.o -MD -MP -MF .deps/libassembly_a-Options.Tpo -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc mv -f .deps/libassembly_a-Options.Tpo .deps/libassembly_a-Options.Po mv -f .deps/libassembly_a-AssemblyAlgorithms.Tpo .deps/libassembly_a-AssemblyAlgorithms.Po rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Assembly' Making all in dialign gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/dialign' depbase=`echo museq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT museq.o -MD -MP -MF $depbase.Tpo -c -o museq.o museq.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo alig.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT alig.o -MD -MP -MF $depbase.Tpo -c -o alig.o alig.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo assemble.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT assemble.o -MD -MP -MF $depbase.Tpo -c -o assemble.o assemble.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo diag.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT diag.o -MD -MP -MF $depbase.Tpo -c -o diag.o diag.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo io.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT io.o -MD -MP -MF $depbase.Tpo -c -o io.o io.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo orf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT orf.o -MD -MP -MF $depbase.Tpo -c -o orf.o orf.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo parameters.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT parameters.o -MD -MP -MF $depbase.Tpo -c -o parameters.o parameters.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo prob.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT prob.o -MD -MP -MF $depbase.Tpo -c -o prob.o prob.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT translate.o -MD -MP -MF $depbase.Tpo -c -o translate.o translate.c &&\ mv -f $depbase.Tpo $depbase.Po alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); ^~~~~~~~ assemble.c:25:39: warning: inline function 'find_diags_guided' declared but never defined extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a cc -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -L/usr/local/lib -o dialign museq.o libdialign.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/dialign' Making all in Align gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Align' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_align-align.o -MD -MP -MF .deps/abyss_align-align.Tpo -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-alignGlobal.o -MD -MP -MF .deps/libalign_a-alignGlobal.Tpo -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dialign.o -MD -MP -MF .deps/libalign_a-dialign.Tpo -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-dna_diag_prob.o -MD -MP -MF .deps/libalign_a-dna_diag_prob.Tpo -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libalign_a-smith_waterman.o -MD -MP -MF .deps/libalign_a-smith_waterman.Tpo -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_mergepairs-mergepairs.o -MD -MP -MF .deps/abyss_mergepairs-mergepairs.Tpo -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc mv -f .deps/libalign_a-dna_diag_prob.Tpo .deps/libalign_a-dna_diag_prob.Po mv -f .deps/libalign_a-alignGlobal.Tpo .deps/libalign_a-alignGlobal.Po mv -f .deps/libalign_a-dialign.Tpo .deps/libalign_a-dialign.Po mv -f .deps/abyss_align-align.Tpo .deps/abyss_align-align.Po mv -f .deps/libalign_a-smith_waterman.Tpo .deps/libalign_a-smith_waterman.Po rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_mergepairs-mergepairs.Tpo .deps/abyss_mergepairs-mergepairs.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Align' Making all in ABYSS gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abyss.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc mv -f .deps/ABYSS-abyss.Tpo .deps/ABYSS-abyss.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' Making all in Bloom gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Bloom' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom-bloom.o -MD -MP -MF .deps/abyss_bloom-bloom.Tpo -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc mv -f .deps/abyss_bloom-bloom.Tpo .deps/abyss_bloom-bloom.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Bloom' Making all in BloomDBG gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_bloom_dbg-bloom-dbg.o -MD -MP -MF .deps/abyss_bloom_dbg-bloom-dbg.Tpo -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc mv -f .deps/abyss_bloom_dbg-bloom-dbg.Tpo .deps/abyss_bloom_dbg-bloom-dbg.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' Making all in Konnector gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Konnector' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT konnector-konnector.o -MD -MP -MF .deps/konnector-konnector.Tpo -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Konnector' Making all in Consensus gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Consensus' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Consensus' Making all in DAssembler gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-DAssembler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-RotatedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.Po mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' Making all in DistanceEst gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-DistanceEst.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-MLE.o -MD -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' Making all in KAligner gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/KAligner' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-KAligner.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-Aligner.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.Po mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/KAligner' Making all in Layout gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Layout' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_layout-layout.o -MD -MP -MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Layout' Making all in LogKmerCount gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT logcounter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' Making all in Map gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Map' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Map' Making all in MergePaths gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergePaths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergeContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' Making all in Overlap gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Overlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Overlap-Overlap.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Overlap' Making all in PairedDBG gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-abyss-paired-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-KmerPair.o -MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o KmerPair.o KmerPair.cc &&\ mv -f $depbase.Tpo $depbase.Po mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.Po rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' Making all in ParseAligns gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ParseAligns-ParseAligns.o -MD -MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' Making all in PathOverlap gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathOverlap-PathOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' Making all in PopBubbles gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' Making all in Scaffold gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_scaffold-scaffold.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_junction-junction.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_longseqdist-longseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_drawgraph-drawgraph.o -MD -MP -MF .deps/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_drawgraph-drawgraph.Tpo .deps/abyss_drawgraph-drawgraph.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' Making all in SimpleGraph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT SimpleGraph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' Making all in kmerprint gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT kmerprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' Making all in FilterGraph gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' Making all in GapFiller gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' Making all in Sealer gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Sealer' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc pandoc -s -o abyss-sealer.1 README.md mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Sealer' Making all in RResolver gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/RResolver' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-RResolverShort.o -MD -MP -MF .deps/abyss_rresolver_short-RResolverShort.Tpo -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-Contigs.o -MD -MP -MF .deps/abyss_rresolver_short-Contigs.Tpo -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-RAlgorithmsShort.o -MD -MP -MF .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-BloomFilters.o -MD -MP -MF .deps/libralgorithmsshort_a-BloomFilters.Tpo -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-Contigs.o -MD -MP -MF .deps/libralgorithmsshort_a-Contigs.Tpo -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-SequenceTree.o -MD -MP -MF .deps/libralgorithmsshort_a-SequenceTree.Tpo -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-RUtils.o -MD -MP -MF .deps/libralgorithmsshort_a-RUtils.Tpo -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp mv -f .deps/libralgorithmsshort_a-RUtils.Tpo .deps/libralgorithmsshort_a-RUtils.Po mv -f .deps/libralgorithmsshort_a-SequenceTree.Tpo .deps/libralgorithmsshort_a-SequenceTree.Po mv -f .deps/abyss_rresolver_short-RResolverShort.Tpo .deps/abyss_rresolver_short-RResolverShort.Po mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po mv -f .deps/libralgorithmsshort_a-Contigs.Tpo .deps/libralgorithmsshort_a-Contigs.Po mv -f .deps/libralgorithmsshort_a-BloomFilters.Tpo .deps/libralgorithmsshort_a-BloomFilters.Po mv -f .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo .deps/libralgorithmsshort_a-RAlgorithmsShort.Po rm -f libralgorithmsshort.a ar cru libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/libdatalayer.a ../Common/libcommon.a /usr/libexec/binutils234/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libralgorithmsshort.a c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/RResolver' Making all in AdjList gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/AdjList' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/construction/biology/abyss/abyss-2.3.1 -isystem /usr/local/include -isystem/construction/biology/abyss/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT AdjList-AdjList.o -MD -MP -MF .deps/AdjList-AdjList.Tpo -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp mv -f .deps/AdjList-AdjList.Tpo .deps/AdjList-AdjList.Po c++ -std=c++11 -Wall -Wextra -Werror -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L/usr/local/lib -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/AdjList' Making all in vendor gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor' Making all in vendor/gtest-1.7.0 gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' Making all in Unittest gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1' pandoc -s -o README.html README.md [WARNING] This document format requires a nonempty element. Defaulting to 'README' as the title. To specify a title, use 'title' in metadata or --metadata title="...". gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' gmake[1]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' SUCCEEDED 00:04:04 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> abyss-2.3.1 depends on executable: bash - found ===> abyss-2.3.1 depends on executable: gmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for abyss-2.3.1 ===> abyss-2.3.1 depends on executable: bash - found ===> abyss-2.3.1 depends on executable: gmake - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/abyss/abyss-2.3.1' Making install in bin gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/bin' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/bin' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -m 555 abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size ABYSS-P '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/bin' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/bin' Making install in doc gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/doc' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/doc' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/share/doc/abyss' install -m 0644 flowchart.pdf flowchart_simplified.pdf '/construction/biology/abyss/stage/usr/local/share/doc/abyss' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/man/man1' install -m 0644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/construction/biology/abyss/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/doc' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/doc' Making install in Common gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Common' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Common' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Common' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Common' Making install in Graph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Graph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Graph' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-gc abyss-todot '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Graph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Graph' Making install in DataLayer gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-fac abyss-tofastq '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataLayer' Making install in DataBase gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataBase' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DataBase' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-db-csv '/construction/biology/abyss/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -m 555 abyss-db-txt '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataBase' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DataBase' Making install in FMIndex gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FMIndex' Making install in Assembly gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Assembly' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Assembly' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Assembly' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Assembly' Making install in dialign gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/dialign' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/dialign' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/dialign' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/dialign' Making install in Align gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Align' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Align' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-align abyss-mergepairs '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Align' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Align' Making install in ABYSS gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 ABYSS '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ABYSS' Making install in Bloom gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Bloom' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Bloom' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-bloom '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Bloom' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Bloom' Making install in BloomDBG gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-bloom-dbg '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/BloomDBG' Making install in Konnector gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Konnector' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Konnector' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 konnector '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Konnector' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Konnector' Making install in Consensus gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Consensus' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Consensus' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 Consensus '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Consensus' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Consensus' Making install in DAssembler gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 DAssembler '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DAssembler' Making install in DistanceEst gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 DistanceEst DistanceEst-ssq '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/DistanceEst' Making install in KAligner gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/KAligner' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/KAligner' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 KAligner '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/KAligner' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/KAligner' Making install in Layout gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Layout' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Layout' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-layout '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Layout' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Layout' Making install in LogKmerCount gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 logcounter '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/LogKmerCount' Making install in Map gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Map' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Map' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-index abyss-map abyss-map-ssq abyss-overlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Map' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Map' Making install in MergePaths gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 MergePaths MergeContigs PathConsensus '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/MergePaths' Making install in Overlap gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Overlap' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Overlap' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 Overlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Overlap' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Overlap' Making install in PairedDBG gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-paired-dbg '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PairedDBG' Making install in ParseAligns gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-fixmate abyss-fixmate-ssq ParseAligns '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/ParseAligns' Making install in PathOverlap gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 PathOverlap '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PathOverlap' Making install in PopBubbles gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 PopBubbles '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/PopBubbles' Making install in Scaffold gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-scaffold abyss-junction abyss-longseqdist '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Scaffold' Making install in SimpleGraph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 SimpleGraph '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/SimpleGraph' Making install in kmerprint gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/kmerprint' Making install in FilterGraph gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-filtergraph '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/FilterGraph' Making install in GapFiller gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-gapfill '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/GapFiller' Making install in Sealer gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Sealer' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Sealer' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-sealer '/construction/biology/abyss/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/man/man1' install -m 0644 abyss-sealer.1 '/construction/biology/abyss/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Sealer' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Sealer' Making install in RResolver gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/RResolver' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/RResolver' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 abyss-rresolver-short '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/RResolver' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/RResolver' Making install in AdjList gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/AdjList' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/AdjList' /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/bin' install -s -m 555 AdjList '/construction/biology/abyss/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/AdjList' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/AdjList' Making install in vendor gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor' Making install in vendor/gtest-1.7.0 gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/vendor/gtest-1.7.0' Making install in Unittest gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1/Unittest' gmake[2]: Entering directory '/construction/biology/abyss/abyss-2.3.1' gmake[3]: Entering directory '/construction/biology/abyss/abyss-2.3.1' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/abyss/stage/usr/local/share/doc/abyss' install -m 0644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md README.html '/construction/biology/abyss/stage/usr/local/share/doc/abyss' gmake[3]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' gmake[2]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' gmake[1]: Leaving directory '/construction/biology/abyss/abyss-2.3.1' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:08 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for abyss-2.3.1 file sizes/checksums [69]: 0% file sizes/checksums [69]: 100% packing files [69]: 0% packing files [69]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:04 TOTAL TIME 00:05:03