====>> Building biology/seqan-apps build started at Sun May 1 14:13:37 UTC 2016 port directory: /usr/ports/biology/seqan-apps building for: FreeBSD 93i386-default-job-01 9.3-RELEASE-p38 FreeBSD 9.3-RELEASE-p38 i386 maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan/Makefile 381791 2015-03-21 11:53:27Z marino $ Poudriere version: 3.2-pre Host OSVERSION: 1100105 Jail OSVERSION: 903000 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 UNAME_v=FreeBSD 9.3-RELEASE-p38 UNAME_r=9.3-RELEASE-p38 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 WARNING_WAIT=0 SAVED_TERM=screen MASTERMNT=/zfs/poudriere/data/.m/93i386-default/ref NO_WARNING_PKG_INSTALL_EOL=yes FORCE_PACKAGE=yes PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=seqan-apps-2.1.1 OLDPWD=/ PWD=/zfs/poudriere/data/.m/93i386-default/ref/.p/pool MASTERNAME=93i386-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.2-pre SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes DEV_WARNING_WAIT=0 OSVERSION=903000 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc49" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing" CPP="cpp49" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49" LIBS="" CXX="g++49" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49" MANPREFIX="/usr/local" PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=9.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --End SUB_LIST-- ---Begin make.conf--- MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### DEFAULT_VERSIONS= ruby=2.2 pgsql=9.5 perl5=5.22 ports-mgmt_poudriere-devel_SET+=QEMU multimedia_ffmpeg_SET+=RTMP X11GRAB FAAC LAME AMR_NB AMR_WB ASS security_gnutls_UNSET+=TPM www_rubygem-passenger_UNSET+=APACHE22 www_rubygem-passenger_SET+=NGINX net-mgmt_collectd5_SET+=CURL NUTUPS PING PGSQL STATGRAB XML net-mgmt_pmacct+=PGSQL security_barnyard2_SET+=PGSQL net_samba41_SET+=PAM_SMBPASS net_samba42_SET+=PAM_SMBPASS net_samba43_SET+=PAM_SMBPASS net_unison240_UNSET+=X11 www_nginx_SET+=PASSENGER HTTP_FANCYINDEX www_owncloud_SET+=PGSQL www_owncloud_UNSET+=SQLITE dns_unbound_SET+=LIBEVENT net-mgmt_zabbix24-frontend_SET+=PGSQL net-mgmt_zabbix24-frontend_UNSET+=MYSQL net-mgmt_zabbix24-proxy_SET+=PGSQL net-mgmt_zabbix24-proxy_UNSET+=MYSQL net-mgmt_zabbix24-server_SET+=PGSQL net-mgmt_zabbix24-server_UNSET+=MYSQL DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =================================================== ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.7.2.txz [93i386-default-job-01] Installing pkg-1.7.2... [93i386-default-job-01] Extracting pkg-1.7.2: .......... done ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.1.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by seqan-apps-2.1.1 for building =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by seqan-apps-2.1.1 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> seqan-apps-2.1.1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by seqan-apps-2.1.1 for building ===> Extracting for seqan-apps-2.1.1 => SHA256 Checksum OK for seqan-seqan-seqan-v2.1.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for seqan-apps-2.1.1 =========================================================================== =================================================== ===> seqan-apps-2.1.1 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.55.0_10.txz [93i386-default-job-01] Installing boost-libs-1.55.0_10... [93i386-default-job-01] `-- Installing libiconv-1.14_9... [93i386-default-job-01] `-- Extracting libiconv-1.14_9: .......... done [93i386-default-job-01] `-- Installing icu-55.1... [93i386-default-job-01] `-- Extracting icu-55.1: .......... done [93i386-default-job-01] Extracting boost-libs-1.55.0_10: .......... done Message from boost-libs-1.55.0_10: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> seqan-apps-2.1.1 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.1.1 ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.5.2.txz [93i386-default-job-01] Installing cmake-3.5.2... [93i386-default-job-01] `-- Installing expat-2.1.0_3... [93i386-default-job-01] `-- Extracting expat-2.1.0_3: .......... done [93i386-default-job-01] `-- Installing cmake-modules-3.5.2... [93i386-default-job-01] `-- Extracting cmake-modules-3.5.2: .......... done [93i386-default-job-01] `-- Installing curl-7.48.0_2... [93i386-default-job-01] | `-- Installing ca_root_nss-3.22.2... [93i386-default-job-01] | `-- Extracting ca_root_nss-3.22.2: ....... done [93i386-default-job-01] `-- Extracting curl-7.48.0_2: .......... done [93i386-default-job-01] `-- Installing libarchive-3.1.2_6,1... [93i386-default-job-01] | `-- Installing lzo2-2.09... [93i386-default-job-01] | `-- Extracting lzo2-2.09: .......... done [93i386-default-job-01] `-- Extracting libarchive-3.1.2_6,1: .......... done [93i386-default-job-01] `-- Installing jsoncpp-0.6.0.r2_2... [93i386-default-job-01] `-- Extracting jsoncpp-0.6.0.r2_2: .......... done [93i386-default-job-01] Extracting cmake-3.5.2: .......... done Message from ca_root_nss-3.22.2: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.1.1 ===> seqan-apps-2.1.1 depends on executable: gcc49 - not found ===> Installing existing package /packages/All/gcc49-4.9.4.s20160427.txz [93i386-default-job-01] Installing gcc49-4.9.4.s20160427... [93i386-default-job-01] `-- Installing indexinfo-0.2.4... [93i386-default-job-01] `-- Extracting indexinfo-0.2.4: .... done [93i386-default-job-01] `-- Installing mpc-1.0.3... [93i386-default-job-01] | `-- Installing gmp-5.1.3_3... [93i386-default-job-01] | `-- Extracting gmp-5.1.3_3: .......... done [93i386-default-job-01] | `-- Installing mpfr-3.1.4... [93i386-default-job-01] | `-- Extracting mpfr-3.1.4: .......... done [93i386-default-job-01] `-- Extracting mpc-1.0.3: ...... done [93i386-default-job-01] `-- Installing gcc-ecj-4.5... [93i386-default-job-01] `-- Extracting gcc-ecj-4.5: . done [93i386-default-job-01] `-- Installing binutils-2.25.1_2,1... [93i386-default-job-01] | `-- Installing gettext-runtime-0.19.7... [93i386-default-job-01] | `-- Extracting gettext-runtime-0.19.7: .......... done [93i386-default-job-01] `-- Extracting binutils-2.25.1_2,1: .......... done [93i386-default-job-01] Extracting gcc49-4.9.4.s20160427: .......... done Message from gcc49-4.9.4.s20160427: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc49 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> seqan-apps-2.1.1 depends on executable: gcc49 - found ===> Returning to build of seqan-apps-2.1.1 ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/as - found ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.2.5.txz [93i386-default-job-01] Installing ccache-3.2.5... [93i386-default-job-01] Extracting ccache-3.2.5: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc49 create symlink for gcc49 (world) create symlink for g++49 create symlink for g++49 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) Message from ccache-3.2.5: NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of seqan-apps-2.1.1 =========================================================================== =================================================== =========================================================================== ====>> Recording filesystem state for prebuild... done =================================================== ===> seqan-apps-2.1.1 depends on package: boost-libs>0 - found ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/cmake - found ===> seqan-apps-2.1.1 depends on executable: gcc49 - found ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/as - found ===> seqan-apps-2.1.1 depends on file: /usr/local/bin/ccache - found ===> Configuring for seqan-apps-2.1.1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build -- The CXX compiler identification is GNU 4.9.4 -- Check for working CXX compiler: /usr/local/libexec/ccache/g++49 -- Check for working CXX compiler: /usr/local/libexec/ccache/g++49 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Initializing SeqAn Build System... -- Performing Test CXX11_DETECTED -- Performing Test CXX11_DETECTED - Success -- Performing Test CXX14_DETECTED -- Performing Test CXX14_DETECTED - Success -- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps -- Configuring apps/seqan_tcoffee -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - not found -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/insegt -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/sak -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/sam2matrix -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/samcat -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/razers3 -- Found BZip2: /usr/lib/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/searchjoin -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/seqcons2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/rep_sep -- Configuring apps/razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/mason2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/tree_recon -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/param_chooser -- Configuring apps/dfi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/snp_store -- Boost version: 1.55.0 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/splazers -- Not building splazers on 32bit architectures. -- Configuring apps/alf -- Configuring apps/pair_align -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/bs_tools -- Boost version: 1.55.0 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/gustaf -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/sgip -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/rabema -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/ngs_roi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/micro_razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/stellar -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/fiona -- Boost version: 1.55.0 -- Not building fiona on 32bit architectures. -- Configuring apps/yara -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) -- Configuring apps/fx_tools -- Unsupported platform FreeBSD, disabling CTD support. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/seqan-apps/work/.build =========================================================================== =================================================== ===> Building for seqan-apps-2.1.1 /usr/local/bin/cmake -H/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 -B/wrkdirs/usr/ports/biology/seqan-apps/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/CMakeFiles/seqan_library.dir/DependInfo.cmake Scanning dependencies of target seqan_library /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build [ 0%] Built target seqan_library /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake Scanning dependencies of target seqan_tcoffee /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build [ 0%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.13.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqan_tcoffee/seqan_tcoffee.cpp [ 1%] Linking CXX executable ../../bin/seqan_tcoffee cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqan_tcoffee && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lpthread [ 1%] Built target seqan_tcoffee /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/insegt /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/insegt /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake Scanning dependencies of target insegt /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build [ 2%] Building CXX object apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/insegt && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.1.5\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/insegt.dir/insegt.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/insegt/insegt.cpp [ 3%] Linking CXX executable ../../bin/insegt cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/insegt && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/insegt.dir/insegt.cpp.o -o ../../bin/insegt -lpthread [ 3%] Built target insegt /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake Scanning dependencies of target sak /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build [ 4%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.4.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sak.dir/sak.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sak/sak.cpp [ 4%] Linking CXX executable ../../bin/sak cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lpthread [ 4%] Built target sak /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sam2matrix /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sam2matrix /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake Scanning dependencies of target sam2matrix /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build [ 4%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sam2matrix && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.3.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/sam2matrix/sam2matrix.cpp [ 5%] Linking CXX executable ../../bin/sam2matrix cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sam2matrix && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lpthread [ 5%] Built target sam2matrix /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/samcat /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake Scanning dependencies of target samcat /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build [ 6%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.3.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/samcat.dir/samcat.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/samcat/samcat.cpp [ 7%] Linking CXX executable ../../bin/samcat cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/samcat && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lpthread -lz [ 7%] Built target samcat /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake Scanning dependencies of target razers3_quality2prob /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build [ 8%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"3.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3/quality2prob.cpp [ 8%] Linking CXX executable ../../bin/razers3_quality2prob cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lpthread -lz -lbz2 [ 8%] Built target razers3_quality2prob /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake Scanning dependencies of target razers3 /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build [ 8%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"3.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/razers.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3/razers.cpp [ 9%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"3.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3/param_tabs.cpp [ 10%] Linking CXX executable ../../bin/razers3 cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lpthread -lz -lbz2 [ 10%] Built target razers3 /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake Scanning dependencies of target razers3_simulate_reads /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build [ 11%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"3.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers3/simulate_reads.cpp [ 12%] Linking CXX executable ../../bin/razers3_simulate_reads cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers3 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lpthread -lz -lbz2 [ 12%] Built target razers3_simulate_reads /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake Scanning dependencies of target s4_join /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build [ 13%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin && /usr/local/libexec/ccache/g++49 -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_join.dir/join.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin/join.cpp [ 13%] Linking CXX executable ../../bin/s4_join cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lpthread [ 13%] Built target s4_join /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake Scanning dependencies of target s4_search /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build [ 14%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin && /usr/local/libexec/ccache/g++49 -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_search.dir/search.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/searchjoin/search.cpp [ 15%] Linking CXX executable ../../bin/s4_search cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/searchjoin && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lpthread [ 15%] Built target s4_search /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake Scanning dependencies of target seqcons2 /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build [ 16%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2/seqcons.cpp [ 17%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2/seqcons_app.cpp [ 17%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/seqcons2/seqcons_options.cpp [ 18%] Linking CXX executable ../../bin/seqcons2 cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/seqcons2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lpthread -lz [ 18%] Built target seqcons2 /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/rep_sep /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/rep_sep /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake Scanning dependencies of target rep_sep /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build [ 19%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/rep_sep && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.1.6\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/rep_sep/rep_sep.cpp [ 19%] Linking CXX executable ../../bin/rep_sep cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/rep_sep && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lpthread [ 19%] Built target rep_sep /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake Scanning dependencies of target razers /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build [ 20%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/razers.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers/razers.cpp [ 21%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.5.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/razers/param_tabs.cpp [ 22%] Linking CXX executable ../../bin/razers cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/razers && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lpthread [ 22%] Built target razers /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake Scanning dependencies of target mason_sim /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build [ 23%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/external_split_merge.cpp [ 24%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/genomic_variants.cpp [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_options.cpp [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/methylation_levels.cpp [ 26%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/simulate_454.cpp [ 27%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/simulate_base.cpp [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/simulate_genome.cpp [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/simulate_illumina.cpp [ 29%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/simulate_sanger.cpp [ 30%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/vcf_materialization.cpp [ 31%] Linking CXX static library libmason_sim.a cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a [ 31%] Built target mason_sim /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake Scanning dependencies of target mason_frag_sequencing /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build [ 31%] Building CXX object apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_frag_sequencing.cpp [ 32%] Linking CXX executable ../../bin/mason_frag_sequencing cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../bin/mason_frag_sequencing -lpthread -lz libmason_sim.a -lpthread -lz [ 32%] Built target mason_frag_sequencing /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake Scanning dependencies of target mason_simulator /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build [ 32%] Building CXX object apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_simulator.cpp [ 33%] Linking CXX executable ../../bin/mason_simulator cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_simulator.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o ../../bin/mason_simulator -lpthread -lz libmason_sim.a -lpthread -lz [ 33%] Built target mason_simulator /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake Scanning dependencies of target mason_genome /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build [ 34%] Building CXX object apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_genome.cpp [ 35%] Linking CXX executable ../../bin/mason_genome cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../bin/mason_genome -lpthread -lz libmason_sim.a -lpthread -lz [ 35%] Built target mason_genome /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake Scanning dependencies of target mason_splicing /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build [ 36%] Building CXX object apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_splicing.cpp [ 37%] Linking CXX executable ../../bin/mason_splicing cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../bin/mason_splicing -lpthread -lz libmason_sim.a -lpthread -lz [ 37%] Built target mason_splicing /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake Scanning dependencies of target mason_materializer /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build [ 37%] Building CXX object apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_materializer.cpp [ 38%] Linking CXX executable ../../bin/mason_materializer cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_materializer.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o ../../bin/mason_materializer -lpthread -lz libmason_sim.a -lpthread -lz [ 38%] Built target mason_materializer /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake Scanning dependencies of target mason_tests /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build [ 38%] Building CXX object apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_tests.cpp [ 39%] Linking CXX executable ../../bin/mason_tests cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../bin/mason_tests -lpthread -lz libmason_sim.a -lpthread -lz [ 39%] Built target mason_tests /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake Scanning dependencies of target mason_methylation /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build [ 40%] Building CXX object apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_methylation.cpp [ 40%] Linking CXX executable ../../bin/mason_methylation cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../bin/mason_methylation -lpthread -lz libmason_sim.a -lpthread -lz [ 40%] Built target mason_methylation /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake Scanning dependencies of target mason_variator /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build [ 41%] Building CXX object apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/mason2/mason_variator.cpp [ 42%] Linking CXX executable ../../bin/mason_variator cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/mason2 && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -fopenmp -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../bin/mason_variator -lpthread -lz libmason_sim.a -lpthread -lz [ 42%] Built target mason_variator /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake Scanning dependencies of target tree_recon /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build [ 43%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.4.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/tree_recon/tree_recon.cpp [ 44%] Linking CXX executable ../../bin/tree_recon cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/tree_recon && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lpthread [ 44%] Built target tree_recon /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/param_chooser /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake Scanning dependencies of target param_chooser /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build [ 45%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/param_chooser/param_chooser.cpp [ 46%] Linking CXX executable ../../bin/param_chooser cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lpthread [ 46%] Built target param_chooser /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/param_chooser /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake Scanning dependencies of target test_funcs_param_chooser /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build [ 46%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"0.0.4\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/param_chooser/test_param_chooser.cpp [ 47%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/param_chooser && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lpthread [ 47%] Built target test_funcs_param_chooser /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/dfi /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/dfi /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake Scanning dependencies of target dfi /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build [ 48%] Building CXX object apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/dfi && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"2.1.5\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/dfi.dir/dfi.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/dfi/dfi.cpp [ 50%] Linking CXX executable ../../bin/dfi cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/dfi && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 /usr/local/libexec/ccache/g++49 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -Wl,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 CMakeFiles/dfi.dir/dfi.cpp.o -o ../../bin/dfi -lpthread [ 50%] Built target dfi /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1 /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake Scanning dependencies of target snp_store /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build [ 50%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/snp_store && /usr/local/libexec/ccache/g++49 -DSEQAN_APP_VERSION=\"1.3.3\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=0 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/include -isystem /usr/local/include -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -std=c++14 -W -Wall -pedantic -fstrict-aliasing -Wstrict-aliasing -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc49 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc49 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:53:0: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h: In function 'double seqan::computeHetTable(THeteroTable&, TOptions&)': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1977:48: error: there are no arguments to 'logl' that depend on a template parameter, so a declaration of 'logl' must be available [-fpermissive] hetTable[n1<<8|n2] = logl(corrected); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1977:48: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h: In function 'double seqan::computeHetTable(THeteroTable&, TOptions&, seqan::MaqMethod&)': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:48: error: there are no arguments to 'expl' that depend on a template parameter, so a declaration of 'expl' must be available [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:64: error: there are no arguments to 'expl' that depend on a template parameter, so a declaration of 'expl' must be available [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:80: error: there are no arguments to 'expl' that depend on a template parameter, so a declaration of 'expl' must be available [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:96: error: there are no arguments to 'expl' that depend on a template parameter, so a declaration of 'expl' must be available [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2023:47: error: there are no arguments to 'logl' that depend on a template parameter, so a declaration of 'logl' must be available [-fpermissive] hetTable[n1<<8|n2] = lC + logl(sum); ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:53:0: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h: In instantiation of 'void seqan::computeCnks(THomoTable&, TDependencies&, TOptions&) [with THomoTable = seqan::String; TDependencies = seqan::String; TOptions = seqan::SNPCallingOptions<>]': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:718:57: required from 'int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:1412:36: required from here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1888:75: error: 'expl' was not declared in this scope sum_a[k] = sum_a[k+1] + expl(lC[n<<8|k] + k*le + (n-k)*le1); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1894:61: error: 'logl' was not declared in this scope q_c[k] = -4.343 * lFks[k] * logl(beta[k] / e); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1900:74: error: 'logl' was not declared in this scope temp[k] = -4.343 * logl(1.0 - expl(lFks[k] * logl(beta[k]))); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1900:75: error: 'expl' was not declared in this scope temp[k] = -4.343 * logl(1.0 - expl(lFks[k] * logl(beta[k]))); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1900:76: error: 'logl' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] temp[k] = -4.343 * logl(1.0 - expl(lFks[k] * logl(beta[k]))); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1900:74: note: 'logl' declared here, later in the translation unit temp[k] = -4.343 * logl(1.0 - expl(lFks[k] * logl(beta[k]))); ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:53:0: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h: In instantiation of 'double seqan::computeHetTable(THeteroTable&, TOptions&) [with THeteroTable = seqan::String; TOptions = seqan::SNPCallingOptions<>]': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:720:103: required from 'int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:1412:36: required from here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:1977:48: error: 'logl' was not declared in this scope hetTable[n1<<8|n2] = logl(corrected); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h: In instantiation of 'double seqan::computeHetTable(THeteroTable&, TOptions&, seqan::MaqMethod&) [with THeteroTable = seqan::String; TOptions = seqan::SNPCallingOptions<>; seqan::MaqMethod = const seqan::Tag]': /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:723:89: required from 'int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]' /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.cpp:1412:36: required from here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:96: error: 'expl' was not declared in this scope sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:80: error: 'expl' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:96: note: 'expl' declared here, later in the translation unit sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:64: error: 'expl' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:96: note: 'expl' declared here, later in the translation unit sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:48: error: 'expl' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2021:96: note: 'expl' declared here, later in the translation unit sum += pk * 0.5 * (expl(log1*n2) * expl(log2*n1) + expl(log1*n1) * expl(log2*n2)); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.1.1/apps/snp_store/snp_store.h:2023:47: error: 'logl' was not declared in this scope hetTable[n1<<8|n2] = lC + logl(sum); ^ *** [apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [apps/snp_store/CMakeFiles/snp_store.dir/all] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [all] Error code 1 Stop in /wrkdirs/usr/ports/biology/seqan-apps/work/.build. *** [do-build] Error code 1 Stop in /usr/ports/biology/seqan-apps. ====>> Cleaning up wrkdir ===> Cleaning for seqan-apps-2.1.1 build of biology/seqan-apps ended at Sun May 1 14:14:23 UTC 2016 build time: 00:00:46 !!! build failure encountered !!!