Date: Sun, 14 Apr 2019 08:35:08 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][biology/freebayes] Failed for freebayes-1.2.0_1 in build Message-ID: <201904140835.x3E8Z8uB043092@pylon.nyi.freebsd.org>
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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 Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/biology/freebayes/Makefile 487272 2018-12-12 01:35:33Z gerald $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p498785_s346161/logs/freebayes-1.2.0_1.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p498785_s346161 Log: =>> Building biology/freebayes build started at Sun Apr 14 08:29:14 UTC 2019 port directory: /usr/ports/biology/freebayes package name: freebayes-1.2.0_1 building for: FreeBSD head-powerpc64-default-job-11 13.0-CURRENT FreeBSD 13.0-CURRENT 1300018 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/freebayes/Makefile 487272 2018-12-12 01:35:33Z gerald $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300012 Jail OSVERSION: 1300018 Job Id: 11 !!! Jail is newer than host. (Jail: 1300018, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300018 UNAME_v=FreeBSD 13.0-CURRENT 1300018 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-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/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/freebayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/freebayes/work HOME=/wrkdirs/usr/ports/biology/freebayes/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/freebayes/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc8" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAG S="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 --std=c++11 -Wl,-rpath=/usr/local/lib/gcc8 " 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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/freebayes" EXAMPLESDIR="share/examples/freebayes" DATADIR="share/freebayes" WWWDIR="www/freebayes" ETCDIR="etc/freebayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/freebayes DOCSDIR=/usr/local/share/doc/freebayes EXAMPLESDIR=/usr/local/share/examples/freebayes WWWDIR=/usr/local/www/freebayes ETCDIR=/usr/local/etc/freebayes --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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300018 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 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 MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> freebayes-1.2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-powerpc64-default-job-11] Installing pkg-1.10.5_5... [head-powerpc64-default-job-11] Extracting pkg-1.10.5_5: .......... done ===> freebayes-1.2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of freebayes-1.2.0_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by freebayes-1.2.0_1 for building => SHA256 Checksum OK for ekg-freebayes-v1.2.0_GH0.tar.gz. => SHA256 Checksum OK for walaj-SeqLib-5941c68_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-bwa-c02766e_GH0.tar.gz. => SHA256 Checksum OK for jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-49fdfbd_GH0.tar.gz. => SHA256 Checksum OK for ekg-bamtools-e77a43f_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-dbb4c51_GH0.tar.gz. => SHA256 Checksum OK for vcflib-vcflib-5e3ce04_GH0.tar.gz. => SHA256 Checksum OK for ekg-fastahack-c68cebb_GH0.tar.gz. => SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz. => SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz. => SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz. => SHA256 Checksum OK for ekg-intervaltree-b704f19_GH0.tar.gz. => SHA256 Checksum OK for ekg-multichoose-73d35da_GH0.tar.gz. => SHA256 Checksum OK for ekg-smithwaterman-84c08d7_GH0.tar.gz. => SHA256 Checksum OK for ekg-tabixpp-80012f8_GH0.tar.gz. => SHA256 Checksum OK for samtools-htslib-0f298ce_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ <snip> DETECTED_VERSION = v1.0.0 CURRENT_VERSION = v1.0.0 cd ../SeqLib/htslib && gmake gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kfunc.o kfunc.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o knetfile.o knetfile.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o kstring.o kstring.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzf.o bgzf.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o errmod.o errmod.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o faidx.o faidx.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile.o hfile.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.5"' > version.h gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o hts.o hts.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o md5.o md5.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o multipart.o multipart.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o probaln.o probaln.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o realn.o realn.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o regidx.o regidx.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o sam.o sam.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf_sweep.o vcf_sweep.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tbx.o tbx.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o textutils.o textutils.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o thread_pool.o thread_pool.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcf.o vcf.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o vcfutils.o vcfutils.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_external.o cram/cram_external.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_index.o cram/cram_index.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_io.o cram/cram_io.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/files.o cram/files.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/mFILE.o cram/mFILE.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/sam_header.o cram/sam_header.c gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o cram/string_alloc.o cram/string_alloc.c /usr/local/bin/ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o /usr/local/bin/ranlib libhts.a gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o bgzip.o bgzip.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o htsfile.o htsfile.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o tabix.o tabix.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hts_endian.o test/hts_endian.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/fieldarith.o test/fieldarith.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/hfile.o test/hfile.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/sam.o test/sam.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_bgzf.o test/test_bgzf.c test/test_bgzf.c: In function 'try_bgzf_dopen': test/test_bgzf.c:137:9: warning: implicit declaration of function 'close'; did you mean 'hclose'? [-Wimplicit-function-declaration] close(fd); ^~~~~ hclose test/test_bgzf.c: In function 'cleanup': test/test_bgzf.c:295:9: warning: implicit declaration of function 'unlink'; did you mean 'unix'? [-Wimplicit-function-declaration] unlink(f->tmp_bgzf); ^~~~~~ unix gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-regidx.o test/test-regidx.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test_view.o test/test_view.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/SeqLib/htslib' cd ../vcflib/tabixpp/ && gmake && cp tabix.hpp ../../src/ gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' g++8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 --std=c++11 -Wl,-rpath=/usr/local/lib/gcc8 -c tabix.cpp -Ihtslib cd htslib && gmake lib-static gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp/htslib' echo '/* Empty config.h generated by Makefile */' > config.h gcc8 -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc8 -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc8 -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc8 -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc8 -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc8 -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc8 -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.1"' > version.h gcc8 -g -Wall -O2 -I. -c -o hts.o hts.c gcc8 -g -Wall -O2 -I. -c -o md5.o md5.c gcc8 -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc8 -g -Wall -O2 -I. -c -o sam.o sam.c sam.c: In function 'bam_hdr_write': sam.c:230:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] strncpy(buf, "BAM\1", 4); ^~~~~~~~~~~~~~~~~~~~~~~~ gcc8 -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc8 -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc8 -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc8 -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc8 -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:2360:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~ cram/cram_io.c:2360:24: note: using the range [0, 4294967295] for directive argument sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~~~~~~~~~~~~~ cram/cram_io.c:2360:24: note: using the range [0, 4294967295] for directive argument cram/cram_io.c:2360:6: note: 'sprintf' output between 11 and 1062 bytes into a destination of size 1024 sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:2252:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(path, path2, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3905:3: cram/cram_io.c:3830:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:3822:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc8 -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc8 -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc8 -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc8 -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc8 -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc8 -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc8 -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc8 -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc8 -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc8 -g -Wall -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c gcc8 -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c gcc8 -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp/htslib' g++8 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc8 --std=c++11 -Wl,-rpath=/usr/local/lib/gcc8 -o tabix++ main.cpp tabix.o -Ihtslib -L. -Lhtslib \ -lhts -lpthread -lm -lz /usr/local/bin/ld: tabix.o: in function `Tabix::~Tabix()': tabix.cpp:(.text+0x70): undefined reference to `hts_itr_destroy' /usr/local/bin/ld: tabix.cpp:(.text+0x7c): undefined reference to `tbx_destroy' /usr/local/bin/ld: tabix.o: in function `Tabix::setRegion(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': tabix.cpp:(.text+0x160): undefined reference to `hts_itr_destroy' /usr/local/bin/ld: tabix.cpp:(.text+0x18c): undefined reference to `hts_itr_querys' /usr/local/bin/ld: tabix.o: in function `Tabix::getHeader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': tabix.cpp:(.text+0x2d0): undefined reference to `hts_getline' /usr/local/bin/ld: tabix.cpp:(.text+0x2f4): undefined reference to `hts_itr_destroy' /usr/local/bin/ld: tabix.cpp:(.text+0x324): undefined reference to `hts_itr_querys' /usr/local/bin/ld: tabix.o: in function `Tabix::Tabix(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': tabix.cpp:(.text+0x488): undefined reference to `bgzf_is_bgzf' /usr/local/bin/ld: tabix.cpp:(.text+0x4e0): undefined reference to `hts_open' /usr/local/bin/ld: tabix.cpp:(.text+0x4f8): undefined reference to `tbx_index_load' /usr/local/bin/ld: tabix.cpp:(.text+0x510): undefined reference to `tbx_seqnames' /usr/local/bin/ld: tabix.cpp:(.text+0x64c): undefined reference to `hts_itr_querys' /usr/local/bin/ld: tabix.o: in function `Tabix::getNextLine(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': tabix.cpp:(.text+0x86c): undefined reference to `hts_get_bgzfp' /usr/local/bin/ld: tabix.cpp:(.text+0x880): undefined reference to `hts_itr_next' /usr/local/bin/ld: tabix.cpp:(.text+0x8d4): undefined reference to `hts_get_bgzfp' /usr/local/bin/ld: tabix.cpp:(.text+0x8e8): undefined reference to `hts_itr_next' /usr/local/bin/ld: tabix.cpp:(.text+0x944): undefined reference to `hts_itr_destroy' /usr/local/bin/ld: tabix.cpp:(.text+0x968): undefined reference to `hts_itr_querys' /usr/local/bin/ld: tabix.cpp:(.text+0x980): undefined reference to `hts_get_bgzfp' /usr/local/bin/ld: tabix.cpp:(.text+0x994): undefined reference to `hts_itr_next' /usr/local/bin/ld: tabix.o:(.toc+0x0): undefined reference to `tbx_readrec' /usr/local/bin/ld: tabix.o:(.toc+0x8): undefined reference to `hts_itr_query' /usr/local/bin/ld: tabix.o:(.toc+0x10): undefined reference to `tbx_name2id' /usr/local/bin/ld: tabix.o:(.toc+0x20): undefined reference to `tbx_conf_vcf' collect2: error: ld returned 1 exit status gmake[4]: *** [Makefile:41: tabix++] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[3]: *** [Makefile:22: all-recur] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/vcflib/tabixpp' gmake[2]: *** [Makefile:202: ../vcflib/tabixpp/tabix.o] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0/src' gmake[1]: *** [Makefile:2: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/freebayes/work/freebayes-1.2.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/freebayes
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