From owner-freebsd-pkg-fallout@freebsd.org Thu Apr 25 00:21:45 2019 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id BD1541585775 for ; Thu, 25 Apr 2019 00:21:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id 4AA158750D for ; Thu, 25 Apr 2019 00:21:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 0F3541585774; Thu, 25 Apr 2019 00:21:44 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id A4E6F1585773 for ; Thu, 25 Apr 2019 00:21:43 +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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 567B58750B for ; Thu, 25 Apr 2019 00:21:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (pylon.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fc]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4557E1BDE9 for ; Thu, 25 Apr 2019 00:21:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (localhost [127.0.0.1]) by pylon.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id x3P0LhGC085132 for ; Thu, 25 Apr 2019 00:21:43 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by pylon.nyi.freebsd.org (8.15.2/8.15.2/Submit) id x3P0LhTJ085105; Thu, 25 Apr 2019 00:21:43 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 25 Apr 2019 00:21:43 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201904250021.x3P0LhTJ085105@pylon.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][biology/star] Failed for STAR-2.7.0.f in build X-Rspamd-Queue-Id: 567B58750B X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.99 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.99)[-0.988,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 25 Apr 2019 00:21:45 -0000 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: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/star/Makefile 499592 2019-04-21 20:30:55Z jwb $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p499706_s346582/logs/STAR-2.7.0.f.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p499706_s346582 Log: =>> Building biology/star build started at Thu Apr 25 00:20:11 UTC 2019 port directory: /usr/ports/biology/star package name: STAR-2.7.0.f building for: FreeBSD head-powerpc64-default-job-19 13.0-CURRENT FreeBSD 13.0-CURRENT 1300020 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/star/Makefile 499592 2019-04-21 20:30:55Z jwb $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300012 Jail OSVERSION: 1300020 Job Id: 19 !!! Jail is newer than host. (Jail: 1300020, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300020 UNAME_v=FreeBSD 13.0-CURRENT 1300020 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/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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=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--- 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=1300020 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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-powerpc64-default-job-19] Installing pkg-1.10.5_5... [head-powerpc64-default-job-19] Extracting pkg-1.10.5_5: .......... done ===> STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - found ===> Returning to build of STAR-2.7.0.f =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user => alexdobin-STAR-2.7.0f_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/alexdobin/STAR/tar.gz/2.7.0f?dummy=/alexdobin-STAR-2.7.0f_GH0.tar.gz fetch: https://codeload.github.com/alexdobin/STAR/tar.gz/2.7.0f?dummy=/alexdobin-STAR-2.7.0f_GH0.tar.gz: size unknown fetch: https://codeload.github.com/alexdobin/STAR/tar.gz/2.7.0f?dummy=/alexdobin-STAR-2.7.0f_GH0.tar.gz: size of remote file is not known alexdobin-STAR-2.7.0f_GH0.tar.gz 7872 kB 5184 kBps 01s ===> Fetching all distfiles required by STAR-2.7.0.f for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by STAR-2.7.0.f for building => SHA256 Checksum OK for alexdobin-STAR-2.7.0f_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by STAR-2.7.0.f for building ===> Extracting for STAR-2.7.0.f => SHA256 Checksum OK for alexdobin-STAR-2.7.0f_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for STAR-2.7.0.f ===> Applying FreeBSD patches for STAR-2.7.0.f =========================================================================== cram/cram_decode.c:1490: warning: comparison between signed and unsigned cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c cram/cram_encode.c: In function 'cram_add_base': cram/cram_encode.c:1584: warning: unused parameter 'fd' cram/cram_encode.c: In function 'cram_add_quality': cram/cram_encode.c:1602: warning: unused parameter 'fd' cram/cram_encode.c: In function 'cram_add_deletion': cram/cram_encode.c:1615: warning: unused parameter 'base' cram/cram_encode.c: In function 'cram_add_hardclip': cram/cram_encode.c:1649: warning: unused parameter 'base' cram/cram_encode.c: In function 'cram_add_skip': cram/cram_encode.c:1659: warning: unused parameter 'base' cram/cram_encode.c: In function 'cram_add_pad': cram/cram_encode.c:1669: warning: unused parameter 'base' cram/cram_encode.c: In function 'cram_encode_aux_1_0': cram/cram_encode.c:1712: warning: unused parameter 'fd' cram/cram_encode.c: In function 'cram_encode_aux': cram/cram_encode.c:1868: warning: unused parameter 'fd' cram/cram_encode.c: In function 'process_one_read': cram/cram_encode.c:2240: warning: comparison between signed and unsigned cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c cram/cram_index.c: In function 'cram_index_load': cram/cram_index.c:99: warning: missing initializer cram/cram_index.c:99: warning: (near initialization for 'kstr.m') cram/cram_index.c: In function 'cram_index_build': cram/cram_index.c:468: warning: comparison between signed and unsigned cc -g -Wall -O2 -O2 -pipe -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: warning: implicit declaration of function 'fsync' cram/cram_io.c: In function 'refs_from_header': cram/cram_io.c:1279: warning: unused parameter 'fd' cram/cram_io.c: In function 'expand_cache_path': cram/cram_io.c:1368: warning: comparison between signed and unsigned cram/cram_io.c:1368: warning: signed and unsigned type in conditional expression cram/cram_io.c: In function 'cram_populate_ref': cram/cram_io.c:1540: warning: comparison between signed and unsigned cram/cram_io.c:1544: warning: implicit declaration of function 'unlink' cram/cram_io.c: In function 'load_ref_portion': cram/cram_io.c:1645: warning: comparison between signed and unsigned cram/cram_io.c: In function 'full_path': cram/cram_io.c:2915: warning: implicit declaration of function 'getcwd' cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c cc -g -Wall -O2 -O2 -pipe -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: warning: empty body in an else-statement cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c cc -g -Wall -O2 -O2 -pipe -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:102: warning: comparison between signed and unsigned cram/mFILE.c:73: warning: unused parameter 'binary' cram/mFILE.c: In function 'mftruncate': cram/mFILE.c:416: warning: signed and unsigned type in conditional expression cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c cram/open_trace_file.c: In function 'find_file_dir': cram/open_trace_file.c:271: warning: comparison between signed and unsigned cram/open_trace_file.c:271: warning: signed and unsigned type in conditional expression cram/open_trace_file.c:272: warning: comparison between signed and unsigned cram/open_trace_file.c:272: warning: signed and unsigned type in conditional expression cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -g -Wall -O2 -O2 -pipe -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: warning: comparison between signed and unsigned cram/sam_header.c: In function 'sam_hdr_vadd': cram/sam_header.c:440: warning: comparison between signed and unsigned cram/sam_header.c: In function 'sam_hdr_find_key': cram/sam_header.c:672: warning: unused parameter 'sh' cram/sam_header.c: In function 'sam_hdr_rebuild': cram/sam_header.c:781: warning: comparison between signed and unsigned cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c cc -g -Wall -O2 -O2 -pipe -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c cc -g -Wall -O2 -O2 -pipe -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 c++ -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Thu Apr 25 00:20:27 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_geneCount sAddAlign.cpp ChimericDetection_chimericDete! ctionMult.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 cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" cc1plus: error: unrecognized command line option "-std=c++11" Makefile:100: Depend.list: No such file or directory gmake[1]: *** [Makefile:99: Depend.list] 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