=>> Building biology/bamutil build started at Sat Mar 30 23:51:41 GMT 2024 port directory: /usr/ports/biology/bamutil package name: bamutil-1.0.15 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 634 Mar 8 2023 /usr/ports/biology/bamutil/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git 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MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamutil/work/.cache HOME=/wrkdirs/usr/ports/biology/bamutil/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/bamutil/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bamutil/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- LIB_PATH_GENERAL=/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen INSTALLDIR=/wrkdirs/usr/ports/biology/bamutil/work/stage/usr/local/bin XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bamutil/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bamutil/work/.cache 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DOCSDIR="share/doc/bamutil" EXAMPLESDIR="share/examples/bamutil" DATADIR="share/bamutil" WWWDIR="www/bamutil" ETCDIR="etc/bamutil" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bamutil DOCSDIR=/usr/local/share/doc/bamutil EXAMPLESDIR=/usr/local/share/examples/bamutil WWWDIR=/usr/local/www/bamutil ETCDIR=/usr/local/etc/bamutil --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamutil-1.0.15 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamutil-1.0.15 for building => SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz. => SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by bamutil-1.0.15 for building ===> Extracting for bamutil-1.0.15 => SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz. => SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for bamutil-1.0.15 ===> Applying FreeBSD patches for bamutil-1.0.15 from /usr/ports/biology/bamutil/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> bamutil-1.0.15 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> bamutil-1.0.15 depends on package: gmake>=4.4.1 - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for bamutil-1.0.15 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for bamutil-1.0.15 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory opt ln -s ../samtools/bgzf.h ../include/bgzf.h ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/knetfile.o -c knetfile.c ar -cr ../libStatGen.a obj/bgzf.o obj/knetfile.o ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h ln -s ../general/BasicHash.h ../include/BasicHash.h ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h ln -s ../general/CharBuffer.h ../include/CharBuffer.h ln -s ../general/Chromosome.h ../include/Chromosome.h ln -s ../general/Cigar.h ../include/Cigar.h ln -s ../general/CigarRoller.h ../include/CigarRoller.h ln -s ../general/Error.h ../include/Error.h ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h ln -s ../general/FileType.h ../include/FileType.h ln -s ../general/FortranFormat.h ../include/FortranFormat.h ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h ln -s ../general/glfHandler.h ../include/glfHandler.h ln -s ../general/GzipFileType.h ../include/GzipFileType.h ln -s ../general/GzipHeader.h ../include/GzipHeader.h ln -s ../general/Hash.h ../include/Hash.h ln -s ../general/IndexBase.h ../include/IndexBase.h ln -s ../general/Input.h ../include/Input.h ln -s ../general/InputFile.h ../include/InputFile.h ln -s ../general/IntArray.h ../include/IntArray.h ln -s ../general/IntHash.h ../include/IntHash.h ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h ln -s ../general/MapFunction.h ../include/MapFunction.h ln -s ../general/MathMatrix.h ../include/MathMatrix.h ln -s ../general/MathVector.h ../include/MathVector.h ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h ln -s ../general/MemoryMap.h ../include/MemoryMap.h ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h ln -s ../general/Parameters.h ../include/Parameters.h ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h ln -s ../general/Pedigree.h ../include/Pedigree.h ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h ln -s ../general/PhoneHome.h ../include/PhoneHome.h ln -s ../general/QuickIndex.h ../include/QuickIndex.h ln -s ../general/Random.h ../include/Random.h ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h ln -s ../general/Sort.h ../include/Sort.h ln -s ../general/STLUtilities.h ../include/STLUtilities.h ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h ln -s ../general/StringAlias.h ../include/StringAlias.h ln -s ../general/StringArray.h ../include/StringArray.h ln -s ../general/StringBasics.h ../include/StringBasics.h ln -s ../general/StringHash.h ../include/StringHash.h ln -s ../general/StringMap.h ../include/StringMap.h ln -s ../general/Tabix.h ../include/Tabix.h ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h ln -s ../general/Constant.h ../include/Constant.h ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h ln -s ../general/Generic.h ../include/Generic.h ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h ln -s ../general/LongHash.h ../include/LongHash.h ln -s ../general/LongInt.h ../include/LongInt.h ln -s ../general/MathConstant.h ../include/MathConstant.h ln -s ../general/PackedVector.h ../include/PackedVector.h ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h ln -s ../general/Performance.h ../include/Performance.h ln -s ../general/ReusableVector.h ../include/ReusableVector.h ln -s ../general/SimpleStats.h ../include/SimpleStats.h ln -s ../general/TrimSequence.h ../include/TrimSequence.h ln -s ../general/UnitTest.h ../include/UnitTest.h c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../bam/SamFile.h ../include/SamFile.h ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h ln -s ../bam/SamInterface.h ../include/SamInterface.h ln -s ../bam/BamInterface.h ../include/BamInterface.h ln -s ../bam/SamRecord.h ../include/SamRecord.h ln -s ../bam/BamIndex.h ../include/BamIndex.h ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h ln -s ../bam/SamValidation.h ../include/SamValidation.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../bam/PileupElement.h ../include/PileupElement.h ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h ln -s ../bam/SamTags.h ../include/SamTags.h ln -s ../bam/PosList.h ../include/PosList.h ln -s ../bam/CigarHelper.h ../include/CigarHelper.h ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h ln -s ../bam/Pileup.h ../include/Pileup.h ln -s ../bam/SamHelper.h ../include/SamHelper.h ln -s ../bam/SamFlag.h ../include/SamFlag.h ln -s ../bam/SamStatus.h ../include/SamStatus.h mkdir -p obj c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ln -s ../fastq/FastQFile.h ../include/FastQFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h mkdir -p obj c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ln -s ../glf/GlfException.h ../include/GlfException.h ln -s ../glf/GlfFile.h ../include/GlfFile.h ln -s ../glf/GlfHeader.h ../include/GlfHeader.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.h ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h ln -s ../glf/GlfStatus.h ../include/GlfStatus.h mkdir -p obj c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o ln -s ../vcf/VcfFile.h ../include/VcfFile.h ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h mkdir -p obj c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o mkdir -p ../obj c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:12 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:15 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Convert.o -c Convert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:17 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Diff.o -c Diff.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:21 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpHeader.o -c DumpHeader.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:23 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitChromosome.o -c SplitChromosome.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:26 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/WriteRegion.o -c WriteRegion.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:28 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpIndex.o -c DumpIndex.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:30 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ReadIndexedBam.o -c ReadIndexedBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:34 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpRefInfo.o -c DumpRefInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:37 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Filter.o -c Filter.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:42 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ReadReference.o -c ReadReference.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:47 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Revert.o -c Revert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Squeeze.o -c Squeeze.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:53 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/FindCigars.o -c FindCigars.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:56 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Stats.o -c Stats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:55:58 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/PileupElementBaseQCStats.o -c PileupElementBaseQCStats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:00 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ClipOverlap.o -c ClipOverlap.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:02 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MateMapByCoord.o -c MateMapByCoord.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:05 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:07 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/TrimBam.o -c TrimBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:10 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/PolishBam.o -c PolishBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:18 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/GapInfo.o -c GapInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:21 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:22 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Bam2FastQ.o -c Bam2FastQ.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:25 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Dedup.o -c Dedup.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:29 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:33 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Prediction.o -c Prediction.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:34 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/LogisticRegression.o -c LogisticRegression.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:36 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MathCholesky.o -c MathCholesky.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:37 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/HashErrorModel.o -c HashErrorModel.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:39 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Recab.o -c Recab.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:42 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/OverlapHandler.o -c OverlapHandler.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:44 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:46 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ExplainFlags.o -c ExplainFlags.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:48 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Main.o -c Main.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:51 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" mkdir -p ../bin c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sat Mar 30 23:56:53 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/bam ../obj/BamExecutable.o ../obj/Validate.o ../obj/Convert.o ../obj/Diff.o ../obj/DumpHeader.o ../obj/SplitChromosome.o ../obj/WriteRegion.o ../obj/DumpIndex.o ../obj/ReadIndexedBam.o ../obj/DumpRefInfo.o ../obj/Filter.o ../obj/ReadReference.o ../obj/Revert.o ../obj/Squeeze.o ../obj/FindCigars.o ../obj/Stats.o ../obj/PileupElementBaseQCStats.o ../obj/ClipOverlap.o ../obj/MateMapByCoord.o ../obj/SplitBam.o ../obj/TrimBam.o ../obj/MergeBam.o ../obj/PolishBam.o ../obj/GapInfo.o ../obj/Logger.o ../obj/Bam2FastQ.o ../obj/Dedup.o ../obj/Dedup_LowMem.o ../obj/Prediction.o ../obj/LogisticRegression.o ../obj/MathCholesky.o ../obj/HashErrorModel.o ../obj/Recab.o ../obj/OverlapHandler.o ../obj/OverlapClipLowerBaseQual.o ../obj/ExplainFlags.o ../obj/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen.a -lm -lz gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory debug mkdir -p obj/debug cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/bgzf.o -c bgzf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/knetfile.o -c knetfile.c ar -cr ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o mkdir -p obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o mkdir -p obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o mkdir -p obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o mkdir -p obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o mkdir -p obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o mkdir -p ../obj/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:08 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:23 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Convert.o -c Convert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:39 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Diff.o -c Diff.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:44 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/DumpHeader.o -c DumpHeader.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:47 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/SplitChromosome.o -c SplitChromosome.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/WriteRegion.o -c WriteRegion.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:53 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/DumpIndex.o -c DumpIndex.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:55 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/ReadIndexedBam.o -c ReadIndexedBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:02:58 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/DumpRefInfo.o -c DumpRefInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:00 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Filter.o -c Filter.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:03 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/ReadReference.o -c ReadReference.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:05 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Revert.o -c Revert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:09 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Squeeze.o -c Squeeze.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/FindCigars.o -c FindCigars.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:17 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Stats.o -c Stats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:21 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/PileupElementBaseQCStats.o -c PileupElementBaseQCStats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:28 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/ClipOverlap.o -c ClipOverlap.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:35 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/MateMapByCoord.o -c MateMapByCoord.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:37 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:42 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/TrimBam.o -c TrimBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:46 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/PolishBam.o -c PolishBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:03:57 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/GapInfo.o -c GapInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:04 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:08 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Bam2FastQ.o -c Bam2FastQ.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:17 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Dedup.o -c Dedup.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:28 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:39 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Prediction.o -c Prediction.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:43 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/LogisticRegression.o -c LogisticRegression.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:04:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/MathCholesky.o -c MathCholesky.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:12 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/HashErrorModel.o -c HashErrorModel.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:26 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Recab.o -c Recab.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:35 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/OverlapHandler.o -c OverlapHandler.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:42 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:48 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/ExplainFlags.o -c ExplainFlags.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:05:55 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/Main.o -c Main.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:06:04 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/debug/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" mkdir -p ../bin/debug c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:06:11 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/debug/bam ../obj/debug/BamExecutable.o ../obj/debug/Validate.o ../obj/debug/Convert.o ../obj/debug/Diff.o ../obj/debug/DumpHeader.o ../obj/debug/SplitChromosome.o ../obj/debug/WriteRegion.o ../obj/debug/DumpIndex.o ../obj/debug/ReadIndexedBam.o ../obj/debug/DumpRefInfo.o ../obj/debug/Filter.o ../obj/debug/ReadReference.o ../obj/debug/Revert.o ../obj/debug/Squeeze.o ../obj/debug/FindCigars.o ../obj/debug/Stats.o ../obj/debug/PileupElementBaseQCStats.o ../obj/debug/ClipOverlap.o ../obj/debug/MateMapByCoord.o ../obj/debug/SplitBam.o ../obj/debug/TrimBam.o ../obj/debug/MergeBam.o ../obj/debug/PolishBam.o ../obj/debug/GapInfo.o ../obj/debug/Logger.o ../obj/debug/Bam2FastQ.o ../obj/debug/Dedup.o ../obj/debug/Dedup_LowMem.o ../obj/debug/Prediction.o ../obj/debug/LogisticRegression.o ../obj/debug/MathCholesky.o ../obj/debug/HashErrorModel.o ../obj/debug/Recab.o ../obj/debug/OverlapHandler.o ../obj/debug/OverlapClipLowerBaseQual.o ../obj/debug/ExplainFlags.o ../obj/debug/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_debug.a -lm -lz gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory profile mkdir -p obj/profile cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/bgzf.o -c bgzf.c cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/knetfile.o -c knetfile.c ar -cr ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o mkdir -p obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o mkdir -p obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o mkdir -p obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o mkdir -p obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o mkdir -p obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" ar -cr ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o mkdir -p ../obj/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:23 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Convert.o -c Convert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:32 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Diff.o -c Diff.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:43 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/DumpHeader.o -c DumpHeader.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/SplitChromosome.o -c SplitChromosome.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:28:58 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/WriteRegion.o -c WriteRegion.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:05 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/DumpIndex.o -c DumpIndex.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:11 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/ReadIndexedBam.o -c ReadIndexedBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:18 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/DumpRefInfo.o -c DumpRefInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:24 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Filter.o -c Filter.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:32 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/ReadReference.o -c ReadReference.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:39 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Revert.o -c Revert.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:48 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Squeeze.o -c Squeeze.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:29:57 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/FindCigars.o -c FindCigars.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:04 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Stats.o -c Stats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:12 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/PileupElementBaseQCStats.o -c PileupElementBaseQCStats.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:21 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/ClipOverlap.o -c ClipOverlap.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:29 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/MateMapByCoord.o -c MateMapByCoord.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:32 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:42 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/TrimBam.o -c TrimBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:30:58 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/PolishBam.o -c PolishBam.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:09 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/GapInfo.o -c GapInfo.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:17 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:21 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Bam2FastQ.o -c Bam2FastQ.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:30 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Dedup.o -c Dedup.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:41 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:31:53 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Prediction.o -c Prediction.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:00 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/LogisticRegression.o -c LogisticRegression.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:08 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/MathCholesky.o -c MathCholesky.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:14 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/HashErrorModel.o -c HashErrorModel.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:22 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Recab.o -c Recab.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:29 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/OverlapHandler.o -c OverlapHandler.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:37 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:45 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/ExplainFlags.o -c ExplainFlags.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:32:51 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/Main.o -c Main.cpp -DVERSION="\"1.0.15\"" c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:33:00 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/profile/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\"" mkdir -p ../bin/profile c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:33:07 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/profile/bam ../obj/profile/BamExecutable.o ../obj/profile/Validate.o ../obj/profile/Convert.o ../obj/profile/Diff.o ../obj/profile/DumpHeader.o ../obj/profile/SplitChromosome.o ../obj/profile/WriteRegion.o ../obj/profile/DumpIndex.o ../obj/profile/ReadIndexedBam.o ../obj/profile/DumpRefInfo.o ../obj/profile/Filter.o ../obj/profile/ReadReference.o ../obj/profile/Revert.o ../obj/profile/Squeeze.o ../obj/profile/FindCigars.o ../obj/profile/Stats.o ../obj/profile/PileupElementBaseQCStats.o ../obj/profile/ClipOverlap.o ../obj/profile/MateMapByCoord.o ../obj/profile/SplitBam.o ../obj/profile/TrimBam.o ../obj/profile/MergeBam.o ../obj/profile/PolishBam.o ../obj/profile/GapInfo.o ../obj/profile/Logger.o ../obj/profile/Bam2FastQ.o ../obj/profile/Dedup.o ../obj/profile/Dedup_LowMem.o ../obj/profile/Prediction.o ../obj/profile/LogisticRegression.o ../obj/profile/MathCholesky.o ../obj/profile/HashErrorModel.o ../obj/profile/Recab.o ../obj/profile/OverlapHandler.o ../obj/profile/OverlapClipLowerBaseQual.o ../obj/profile/ExplainFlags.o ../obj/profile/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_profile.a -lm -lz gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for bamutil-1.0.15 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory opt ar -cr ../libStatGen.a obj/bgzf.o obj/knetfile.o ar -cr ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ar -cr ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ar -cr ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ar -cr ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o ar -cr ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:33:32 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/bam ../obj/BamExecutable.o ../obj/Validate.o ../obj/Convert.o ../obj/Diff.o ../obj/DumpHeader.o ../obj/SplitChromosome.o ../obj/WriteRegion.o ../obj/DumpIndex.o ../obj/ReadIndexedBam.o ../obj/DumpRefInfo.o ../obj/Filter.o ../obj/ReadReference.o ../obj/Revert.o ../obj/Squeeze.o ../obj/FindCigars.o ../obj/Stats.o ../obj/PileupElementBaseQCStats.o ../obj/ClipOverlap.o ../obj/MateMapByCoord.o ../obj/SplitBam.o ../obj/TrimBam.o ../obj/MergeBam.o ../obj/PolishBam.o ../obj/GapInfo.o ../obj/Logger.o ../obj/Bam2FastQ.o ../obj/Dedup.o ../obj/Dedup_LowMem.o ../obj/Prediction.o ../obj/LogisticRegression.o ../obj/MathCholesky.o ../obj/HashErrorModel.o ../obj/Recab.o ../obj/OverlapHandler.o ../obj/OverlapClipLowerBaseQual.o ../obj/ExplainFlags.o ../obj/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen.a -lm -lz gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory debug ar -cr ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar -cr ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ar -cr ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o ar -cr ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ar -cr ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ar -cr ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:33:50 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/debug/bam ../obj/debug/BamExecutable.o ../obj/debug/Validate.o ../obj/debug/Convert.o ../obj/debug/Diff.o ../obj/debug/DumpHeader.o ../obj/debug/SplitChromosome.o ../obj/debug/WriteRegion.o ../obj/debug/DumpIndex.o ../obj/debug/ReadIndexedBam.o ../obj/debug/DumpRefInfo.o ../obj/debug/Filter.o ../obj/debug/ReadReference.o ../obj/debug/Revert.o ../obj/debug/Squeeze.o ../obj/debug/FindCigars.o ../obj/debug/Stats.o ../obj/debug/PileupElementBaseQCStats.o ../obj/debug/ClipOverlap.o ../obj/debug/MateMapByCoord.o ../obj/debug/SplitBam.o ../obj/debug/TrimBam.o ../obj/debug/MergeBam.o ../obj/debug/PolishBam.o ../obj/debug/GapInfo.o ../obj/debug/Logger.o ../obj/debug/Bam2FastQ.o ../obj/debug/Dedup.o ../obj/debug/Dedup_LowMem.o ../obj/debug/Prediction.o ../obj/debug/LogisticRegression.o ../obj/debug/MathCholesky.o ../obj/debug/HashErrorModel.o ../obj/debug/Recab.o ../obj/debug/OverlapHandler.o ../obj/debug/OverlapClipLowerBaseQual.o ../obj/debug/ExplainFlags.o ../obj/debug/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_debug.a -lm -lz gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory profile ar -cr ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar -cr ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ar -cr ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o ar -cr ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ar -cr ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o ar -cr ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Sun Mar 31 00:34:10 UTC 2024\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/profile/bam ../obj/profile/BamExecutable.o ../obj/profile/Validate.o ../obj/profile/Convert.o ../obj/profile/Diff.o ../obj/profile/DumpHeader.o ../obj/profile/SplitChromosome.o ../obj/profile/WriteRegion.o ../obj/profile/DumpIndex.o ../obj/profile/ReadIndexedBam.o ../obj/profile/DumpRefInfo.o ../obj/profile/Filter.o ../obj/profile/ReadReference.o ../obj/profile/Revert.o ../obj/profile/Squeeze.o ../obj/profile/FindCigars.o ../obj/profile/Stats.o ../obj/profile/PileupElementBaseQCStats.o ../obj/profile/ClipOverlap.o ../obj/profile/MateMapByCoord.o ../obj/profile/SplitBam.o ../obj/profile/TrimBam.o ../obj/profile/MergeBam.o ../obj/profile/PolishBam.o ../obj/profile/GapInfo.o ../obj/profile/Logger.o ../obj/profile/Bam2FastQ.o ../obj/profile/Dedup.o ../obj/profile/Dedup_LowMem.o ../obj/profile/Prediction.o ../obj/profile/LogisticRegression.o ../obj/profile/MathCholesky.o ../obj/profile/HashErrorModel.o ../obj/profile/Recab.o ../obj/profile/OverlapHandler.o ../obj/profile/OverlapClipLowerBaseQual.o ../obj/profile/ExplainFlags.o ../obj/profile/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_profile.a -lm -lz Installing to directory /wrkdirs/usr/ports/biology/bamutil/work/stage/usr/local/bin To select a different directory, run make install INSTALLDIR=your_preferred_dir cp ../bin/bam /wrkdirs/usr/ports/biology/bamutil/work/stage/usr/local/bin gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-03-30T23:51:41+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for bamutil-1.0.15 ===> Building bamutil-1.0.15 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for bamutil-1.0.15 build of biology/bamutil | bamutil-1.0.15 ended at Sun Mar 31 00:34:23 GMT 2024 build time: 00:42:43