[package - main-amd64-default][biology/bamutil] Failed for bamutil-1.0.15 in build
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Date: Sun, 11 Dec 2022 09:19:35 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p34cc6c5bcc7c_s08b05de1e2/logs/bamutil-1.0.15.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p34cc6c5bcc7c_s08b05de1e2 Log: =>> Building biology/bamutil build started at Sun Dec 11 09:14:37 UTC 2022 port directory: /usr/ports/biology/bamutil package name: bamutil-1.0.15 building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400074 amd64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400074 Job Id: 10 !!! Jail is newer than host. (Jail: 1400074, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400074 UNAME_v=FreeBSD 14.0-CURRENT 1400074 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- 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=/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 --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 HOME=/wrkdirs/usr/ports/biology/bamutil/work TMPDIR="/tmp" PATH=/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 MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX= "/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400074 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---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) 1024 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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.18.4.pkg [main-amd64-default-job-10] Installing pkg-1.18.4... [main-amd64-default-job-10] Extracting pkg-1.18.4: .......... done ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bamutil-1.0.15 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> 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. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> 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. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for bamutil-1.0.15 ===> Applying FreeBSD patches for bamutil-1.0.15 from /usr/ports/biology/bamutil/files =========================================================================== =======================<phase: build-depends >============================ ===> bamutil-1.0.15 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg <snip> c++ -O2 -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/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/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/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/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/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/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/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/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/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/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/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/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/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/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\"" c++ -O2 -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_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 mkdir -p ../bin/debug gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory profile mkdir -p obj/profile 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 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 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/knetfile.o -c knetfile.c mkdir -p ../bin/profile ar -cr ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.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 Dec 11 09:17:26 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\"" 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/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 Dec 11 09:17:26 UTC 2022\"" -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../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/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 Dec 11 09:17:32 UTC 2022\"" -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../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/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 Dec 11 09:17:38 UTC 2022\"" -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../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/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 Dec 11 09:17:44 UTC 2022\"" -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../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/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 Dec 11 09:17:48 UTC 2022\"" -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../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/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 Dec 11 09:17:53 UTC 2022\"" -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../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/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 Dec 11 09:17:57 UTC 2022\"" -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../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/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 Dec 11 09:18:00 UTC 2022\"" -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../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/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 Dec 11 09:18:02 UTC 2022\"" -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../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/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 Dec 11 09:18:07 UTC 2022\"" -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../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/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 Dec 11 09:18:11 UTC 2022\"" -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../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/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 Dec 11 09:18:14 UTC 2022\"" -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../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/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 Dec 11 09:18:18 UTC 2022\"" -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../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/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 Dec 11 09:18:22 UTC 2022\"" -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../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/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 Dec 11 09:18:26 UTC 2022\"" -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../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/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 Dec 11 09:18:30 UTC 2022\"" -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../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/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 Dec 11 09:18:33 UTC 2022\"" -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../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/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 Dec 11 09:18:36 UTC 2022\"" -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../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/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 Dec 11 09:18:39 UTC 2022\"" -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../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/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 Dec 11 09:18:42 UTC 2022\"" -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../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/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 Dec 11 09:18:44 UTC 2022\"" -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../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\"" 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/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/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/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/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/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/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 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 Dec 11 09:18:48 UTC 2022\"" -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../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\"" 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/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/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/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/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/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/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 c++ -O2 -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\"" 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" c++ -O2 -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/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 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: fatal: Incorrect file header signature: Invalid argument gmake[4]: *** [../Makefiles/Makefile.lib:41: ../libStatGen_profile.a] Error 1 gmake[3]: *** [Makefiles/Makefile.base:15: bam] Error 2 gmake[3]: *** Waiting for unfinished jobs.... 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 Dec 11 09:18:56 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\"" gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:54: /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_profile.a] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src' gmake[1]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.base:15: src] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/bamutil