From nobody Thu Jul 27 06:13:52 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RBL7P3jCHz4nyGC for ; Thu, 27 Jul 2023 06:13:53 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4RBL7N6LYDz3kWn for ; Thu, 27 Jul 2023 06:13:52 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1690438432; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=F/cgftNAE2ncE2OvIEED0sQNkEzePXNqFhUD2X669bI=; b=jgEgXCdpOW5oV1F1xmamOGc/T9Y8Ovmr/6/oBnRhGWAaiaDStDnGscuCixaMdXh4tCHi52 wibHOhvsLh7PCaZ+hXkCmqDDkVUNr7b6RyskzRi/I4nTqQh5+FYSoR4TpEjYSEYdgCNuzb Q35HMhNWCn2kGAAgMeXvCgL3z0M3eKfozuZGhKSthXwaKZ5x3z8oIc75mSaC6ryNQBiCS0 C0to65Jj4F/FG4CgOI5DYKvt92Uh0BB67lIHEfCekqO2+PNmj31W8/K3yv8d/QAiGUux5Z n9qtrey9uMt7zCqlotnKJtMi1xfMqx8LV/rNIXbLDaY6aqtIYCHh1cvZ4Prvlw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1690438432; a=rsa-sha256; cv=none; b=M8wY9fxmzamqnqsfocPFfsgBnFEEKnZ+j0TxRu6prYi1QPqFC+KooPlCey2YncEk9pAG40 B+awGkNgBEEyRtkyPp96ywcvhwS2RlqXWxaHf1qn8PhqOVuBr33EQOYgD6MNL2EP3OkcQW zHRJhJ0/S9VB20kKYZzJSd42ZGcR+I1AZ/1d1ajMucouJ2HhoTOIQ6nEoR+Q0nlKpoRI8a hdVXqc0dBYVD13i1Kmksiddiv0+HHt1RgGa8dn3ZXXcYUx1rgcjoNlNXM18+U+5NqiGI1Q e1cRGLKHh+hD/M/WMyKhtJLLB8G6lxJjjEVKHHGI96x5s4Ko85us8GAnFf5/fw== Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:17]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4RBL7N54Nsz1D4C for ; Thu, 27 Jul 2023 06:13:52 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id ed2f by beefy8.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy8.nyi.freebsd.org); Thu, 27 Jul 2023 06:13:52 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - main-armv6-default][biology/bamutil] Failed for bamutil-1.0.15 in build Date: Thu, 27 Jul 2023 06:13:52 +0000 Message-Id: <64c20b20.ed2f.6ab335@beefy8.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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/beefy8/data/main-armv6-default/p5cfda4f9e5a4_s474708c334/logs/bamutil-1.0.15.log Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p5cfda4f9e5a4_s474708c334 Log: =>> Building biology/bamutil build started at Thu Jul 27 04:57:25 UTC 2023 port directory: /usr/ports/biology/bamutil package name: bamutil-1.0.15 building for: FreeBSD main-armv6-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400088 Jail OSVERSION: 1400093 Job Id: 07 !!! Jail is newer than host. (Jail: 1400093, Host: 1400088) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv6-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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /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_9d218390=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_53255a77=yes CC_OUTPUT_9d218390_911cfe02=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes CC_OUTPUT_9d218390_af59ad06=yes CC_OUTPUT_9d218390_a15f3fcf=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-armv6-default-job-07] Installing pkg-1.20.4... [main-armv6-default-job-07] Extracting pkg-1.20.4: .......... done ===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bamutil-1.0.15 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bamutil-1.0.15 for building c++ -O2 -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\"" In file included from ReferenceSequence.cpp:25: ./ReferenceSequence.h:315:39: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while((ch = inputStream.ifgetc()) != EOF) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ ./ReferenceSequence.h:327:68: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while (!isspace((ch = inputStream.ifgetc())) && ch != EOF) ~~ ^ ~~~ ./ReferenceSequence.h:336:28: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] } while(ch != EOF && ch != '\n' && ch != '\r'); ~~ ^ ~~~ 3 warnings generated. c++ -O2 -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="\"Thu Jul 27 05:49:56 UTC 2023\"" -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="\"Thu Jul 27 05:50:39 UTC 2023\"" -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="\"Thu Jul 27 05:51:14 UTC 2023\"" -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="\"Thu Jul 27 05:52:08 UTC 2023\"" -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="\"Thu Jul 27 05:52:39 UTC 2023\"" -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="\"Thu Jul 27 05:53:10 UTC 2023\"" -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="\"Thu Jul 27 05:53:50 UTC 2023\"" -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="\"Thu Jul 27 05:54:20 UTC 2023\"" -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="\"Thu Jul 27 05:54:51 UTC 2023\"" -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="\"Thu Jul 27 05:55:23 UTC 2023\"" -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="\"Thu Jul 27 05:55:59 UTC 2023\"" -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="\"Thu Jul 27 05:56:31 UTC 2023\"" -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="\"Thu Jul 27 05:57:04 UTC 2023\"" -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="\"Thu Jul 27 05:57:44 UTC 2023\"" -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="\"Thu Jul 27 05:58:16 UTC 2023\"" -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="\"Thu Jul 27 05:58:59 UTC 2023\"" -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="\"Thu Jul 27 05:59:30 UTC 2023\"" -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="\"Thu Jul 27 06:00:07 UTC 2023\"" -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="\"Thu Jul 27 06:00:40 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\"" SplitBam.cpp:119:101: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while ( ( c = getopt_long(argc-1, &(argv[1]), "i:o:vLn:", getopt_long_options, &n_option_index) ) != -1 ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ 1 warning generated. 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="\"Thu Jul 27 06:01:18 UTC 2023\"" -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="\"Thu Jul 27 06:01:53 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\"" MergeBam.cpp:150:99: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare] while ( ( c = getopt_long(argc, argv, "l:i:o:vIL:r:R:", getopt_long_options, &n_option_index) ) != -1 ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~ 1 warning generated. 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="\"Thu Jul 27 06:02:50 UTC 2023\"" -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="\"Thu Jul 27 06:03:49 UTC 2023\"" -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="\"Thu Jul 27 06:04:31 UTC 2023\"" -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="\"Thu Jul 27 06:04:58 UTC 2023\"" -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="\"Thu Jul 27 06:05:49 UTC 2023\"" -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="\"Thu Jul 27 06:06:55 UTC 2023\"" -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="\"Thu Jul 27 06:08:00 UTC 2023\"" -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="\"Thu Jul 27 06:08:31 UTC 2023\"" -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="\"Thu Jul 27 06:09:00 UTC 2023\"" -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="\"Thu Jul 27 06:09:26 UTC 2023\"" -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="\"Thu Jul 27 06:10:06 UTC 2023\"" -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="\"Thu Jul 27 06:10:58 UTC 2023\"" -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="\"Thu Jul 27 06:11:31 UTC 2023\"" -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="\"Thu Jul 27 06:12:03 UTC 2023\"" -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="\"Thu Jul 27 06:12:36 UTC 2023\"" -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="\"Thu Jul 27 06:13:23 UTC 2023\"" -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="\"Thu Jul 27 06:13:49 UTC 2023\"" -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/OverlapHan dler.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 c++: error: unable to execute command: Abort trap (core dumped) c++: error: linker command failed due to signal (use -v to see invocation) gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:40: ../bin/bam] Error 1 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' *** Error code 1 Stop. make: stopped in /usr/ports/biology/bamutil