Date: Tue, 10 Sep 2019 09:55:25 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv7-default][biology/star] Failed for rna-STAR-2.7.0.f_1 in build Message-ID: <201909100955.x8A9tPlW005077@beefy16.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/star/Makefile 507372 2019-07-26 20:46:53Z gerald $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p511388_s351963/logs/rna-STAR-2.7.0.f_1.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p511388_s351963 Log: =>> Building biology/star build started at Tue Sep 10 09:41:56 UTC 2019 port directory: /usr/ports/biology/star package name: rna-STAR-2.7.0.f_1 building for: FreeBSD head-armv7-default-job-16 13.0-CURRENT FreeBSD 13.0-CURRENT 1300046 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/star/Makefile 507372 2019-07-26 20:46:53Z gerald $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300031 Jail OSVERSION: 1300046 Job Id: 16 !!! Jail is newer than host. (Jail: 1300046, Host: 1300031) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300046 UNAME_v=FreeBSD 13.0-CURRENT 1300046 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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="gcc9" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing " CPP="cpp9" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 " LIBS="" CXX="g++9" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 " 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/STAR" EXAMPLESDIR="share/examples/STAR" DATADIR="share/STAR" WWWDIR="www/STAR" ETCDIR="etc/STAR" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/STAR DOCSDIR=/usr/local/share/doc/STAR EXAMPLESDIR=/usr/local/share/examples/STAR WWWDIR=/usr/local/www/STAR ETCDIR=/usr/local/etc/STAR --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=armv7 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 # 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_9d218390=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: armv7-unknown-freebsd13.0-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_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300046 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as 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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> rna-STAR-2.7.0.f_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz [head-armv7-default-job-16] Installing pkg-1.11.1... [head-armv7-default-job-16] Extracting pkg-1.11.1: .......... done ===> rna-STAR-2.7.0.f_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of rna-STAR-2.7.0.f_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user <snip> gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c: In function 'paranoid_fclose': cram/cram_io.c:1006:15: warning: implicit declaration of function 'fsync' [-Wimplicit-function-declaration] 1006 | if (-1 == fsync(fileno(fp))) { | ^~~~~ cram/cram_io.c: In function 'refs_from_header': cram/cram_io.c:1279:49: warning: unused parameter 'fd' [-Wunused-parameter] 1279 | static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) { | ~~~~~~~~~^~ In file included from ./cram/cram_io.h:52, from ./cram/cram.h:55, from cram/cram_io.c:65: cram/cram_io.c: In function 'expand_cache_path': ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^ cram/cram_io.c:1368:10: note: in expansion of macro 'MIN' 1368 | l = MIN(l, strlen(fn)); | ^~~ ./cram/misc.h:103:36: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^~~ cram/cram_io.c:1368:10: note: in expansion of macro 'MIN' 1368 | l = MIN(l, strlen(fn)); | ^~~ cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:1544:6: warning: implicit declaration of function 'unlink' [-Wimplicit-function-declaration] 1544 | unlink(path_tmp); | ^~~~~~ cram/cram_io.c: In function 'full_path': cram/cram_io.c:2915:7: warning: implicit declaration of function 'getcwd'; did you mean 'getw'? [-Wimplicit-function-declaration] 2915 | if (!getcwd(out, PATH_MAX) || | ^~~~~~ | getw cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:1529:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1529 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); | ^~~~~ cram/cram_io.c:1529:24: note: directive argument in the range [0, 2147483647] 1529 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); | ^~~~~~~~~~~ cram/cram_io.c:1529:6: note: 'sprintf' output between 7 and 1039 bytes into a destination of size 1024 1529 | sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:2987:3: cram/cram_io.c:2917:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 2917 | strncpy(out, in, PATH_MAX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c:2909:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] 2909 | strncpy(out, in, PATH_MAX); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram/cram_io.c: In function 'cram_dopen': cram/cram_io.c:3291:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation] 3291 | strncpy(def.file_id, filename, 20); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c cram/cram_stats.c: In function 'cram_stats_add': cram/cram_stats.c:74:6: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] 74 | ; // FIXME: handle error | ^ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c cram/mFILE.c: In function 'mfload': cram/mFILE.c:73:65: warning: unused parameter 'binary' [-Wunused-parameter] 73 | static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) { | ~~~~^~~~~~ cram/mFILE.c: In function 'mftruncate': cram/mFILE.c:416:31: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 416 | mf->size = offset != -1 ? offset : mf->offset; | ^~~~~~ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c In file included from cram/open_trace_file.c:81: cram/open_trace_file.c: In function 'find_file_dir': ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^ cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN' 271 | path_end += MIN(strlen(file), l); | ^~~ ./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^~~ cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN' 271 | path_end += MIN(strlen(file), l); | ^~~ ./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^ cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN' 272 | file += MIN(strlen(file), l); | ^~~ ./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^~~ cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN' 272 | file += MIN(strlen(file), l); | ^~~ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c cram/sam_header.c: In function 'sam_hdr_add_lines': cram/sam_header.c:320:9: warning: comparison of integer expressions of different signedness: 'int' and 'khint_t' {aka 'unsigned int'} [-Wsign-compare] 320 | if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new))) | ^~ cram/sam_header.c: In function 'sam_hdr_vadd': cram/sam_header.c:440:12: warning: comparison of integer expressions of different signedness: 'int' and 'khint32_t' {aka 'unsigned int'} [-Wsign-compare] 440 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) | ^~ cram/sam_header.c: In function 'sam_hdr_find_key': cram/sam_header.c:672:40: warning: unused parameter 'sh' [-Wunused-parameter] 672 | SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh, | ~~~~~~~~~^~ cram/sam_header.c: In function 'sam_hdr_rebuild': cram/sam_header.c:781:24: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 781 | if (kh_key(hdr->h, k) == K("HD")) | ^~ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cram/vlen.c: In function 'vflen': cram/vlen.c:121:9: warning: variable 'i' set but not used [-Wunused-but-set-variable] 121 | int i; | ^ gcc9 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -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 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_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source/htslib' echo ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSpli t.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput. cpp ReadAlign_mapOneRead.cpp ReadAlign_outpu! tTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp R eadAlign_mapOneRead.cpp ReadAlign_outputTran! scriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c 'rm' -f ./Depend.list g++9 -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:42:22 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -MM ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters .cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCoun tsAddAlign.cpp ChimericDetection_chimericDet! ectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list g++9: warning: parametersDefault.xxd: linker input file unused because linking not done g++9: warning: htslib: linker input file unused because linking not done g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ParametersSolo.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloRead.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloRead_record.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadBarcode.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadBarcode_getCBandUMI.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature_record.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloReadFeature_inputRecords.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 Solo.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_collapseUMI.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_outputResults.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SoloFeature_processRecords.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ReadAlign_outputAlignments.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 ReadAlign.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 STAR.cpp In file included from /usr/local/lib/gcc9/include/c++/vector:72, from IncludeDefine.h:14, from STAR.cpp:4: /usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]': /usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]': /usr/local/lib/gcc9/include/c++/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SharedMemory.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 PackedArray.cpp g++9 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 10 09:50:47 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 SuffixArrayFuns.cpp In file included from SuffixArrayFuns.h:4, from SuffixArrayFuns.cpp:1: SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)': IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'? 58 | #define uint128 __uint128_t | ^~~~~~~~~~~ SuffixArrayFuns.cpp:350:18: note: in expansion of macro 'uint128' 350 | register uint128 g1=*( (uint128*) (gSeq+SAstr) ); | ^~~~~~~ SuffixArrayFuns.cpp:353:37: error: 'g1' was not declared in this scope; did you mean 'g2'? 353 | register char g2=(char) g1; | ^~ | g2 In file included from SuffixArrayFuns.h:4, from SuffixArrayFuns.cpp:1: IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'? 58 | #define uint128 __uint128_t | ^~~~~~~~~~~ SuffixArrayFuns.cpp:367:18: note: in expansion of macro 'uint128' 367 | register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) ); | ^~~~~~~ SuffixArrayFuns.cpp:370:38: error: 'g1' was not declared in this scope; did you mean 'g2'? 370 | register char g2=(char) (g1>>(8*(15-ii))); | ^~ | g2 SuffixArrayFuns.cpp:341:29: warning: unused parameter 'gSeq' [-Wunused-parameter] 341 | uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Genome &mapGen, uint iSA, int L, int & iL4) | ~~~~~~^~~~ gmake[1]: *** [Makefile:66: SuffixArrayFuns.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source' *** Error code 1 Stop. make: stopped in /usr/ports/biology/star
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