Attachment 659126 Details for Bug 741152 – build.log

build.log

build.log (text/plain), 36.75 KB, created by Agostino Sarubbo on 2020-09-08 09:34:44 UTC

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Creator: Agostino Sarubbo

Created: 2020-09-08 09:34:44 UTC

Size: 36.75 KB

patch

obsolete

> * Package:    sci-biology/STAR-2.5.3a
> * Repository: gentoo
> * Maintainer: sci-biology@gentoo.org
> * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
> * FEATURES:   network-sandbox preserve-libs sandbox test userpriv usersandbox
>
>
>@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@
>This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix;
>This ebuild was merged at the following commit:
>https://github.com/gentoo-mirror/gentoo/commit/264d774b2f6baba0736c85dfc22e149187c467cd  (Tue Sep  8 07:35:30 UTC 2020)
>@@@@@ END @@@@@
>
>
>
>emerge --info:
>Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64)
>=================================================================
>System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5
>KiB Mem:    64359960 total,  29494212 free
>KiB Swap:          0 total,         0 free
>Timestamp of repository gentoo: Tue, 08 Sep 2020 07:35:29 +0000
>sh bash 5.0_p18
>ld GNU ld (Gentoo 2.34 p6) 2.34.0
>app-shells/bash:          5.0_p18::gentoo
>dev-lang/perl:            5.30.3-r1::gentoo
>dev-lang/python:          2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo
>dev-util/cmake:           3.18.2::gentoo
>sys-apps/baselayout:      2.7::gentoo
>sys-apps/openrc:          0.42.1::gentoo
>sys-apps/sandbox:         2.20::gentoo
>sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
>sys-devel/automake:       1.16.2::gentoo
>sys-devel/binutils:       2.34-r2::gentoo
>sys-devel/gcc:            10.2.0-r1::gentoo
>sys-devel/gcc-config:     2.3.2::gentoo
>sys-devel/libtool:        2.4.6-r6::gentoo
>sys-devel/make:           4.3::gentoo
>sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers)
>sys-libs/glibc:           2.32-r1::gentoo
>Repositories:
>
>gentoo
>    location: /usr/portage
>    sync-type: rsync
>    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
>    priority: -1000
>    sync-rsync-extra-opts: 
>    sync-rsync-verify-jobs: 1
>    sync-rsync-verify-max-age: 24
>    sync-rsync-verify-metamanifest: yes
>
>ACCEPT_KEYWORDS="amd64 ~amd64"
>ACCEPT_LICENSE="* GPL-3"
>CBUILD="x86_64-pc-linux-gnu"
>CC="x86_64-pc-linux-gnu-clang"
>CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
>CHOST="x86_64-pc-linux-gnu"
>CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
>CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
>CXX="x86_64-pc-linux-gnu-clang++"
>CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
>DISTDIR="/var/tmp/portage/sci-biology/STAR-2.5.3a/distdir"
>EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k"
>ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
>FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
>FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
>FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color"
>GENTOO_MIRRORS="http://distfiles.gentoo.org"
>LANG="C.UTF-8"
>LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld"
>MAKEOPTS="-j16 V=1"
>PKGDIR="/root/.packages"
>PORTAGE_CONFIGROOT="/"
>PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
>PORTAGE_TMPDIR="/var/tmp"
>USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU"
>Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
>
>
>
>>>> Unpacking source...
>>>> Unpacking STAR-2.5.3a.tar.gz to /var/tmp/portage/sci-biology/STAR-2.5.3a/work
>>>> Source unpacked in /var/tmp/portage/sci-biology/STAR-2.5.3a/work
>>>> Preparing source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
> * Applying STAR-2.5.3a-fix-build-system.patch ...
> [ ok ]
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a ...
>make -j16 V=1 -C source STAR 
>make: Entering directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source'
>echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
>BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
>/bin/rm -f ./Depend.list
>x86_64-pc-linux-gnu-clang++ -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:01 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.cpp Chain.cpp ErrorWarning.cpp Genome.cpp Genome_insertSequences.cpp GlobalVariables.cpp InOutStreams.cpp OutSJ.cpp PackedArray.cpp Parameters.cpp Parameters_closeReadsFiles.cpp Parameters_openReadsFiles.cpp Quantifications.cpp ReadAlign.cpp ReadAlignChunk.cpp ReadAlignChunk_mapChunk.cpp ReadAlignChunk_processChunks.cpp ReadAlign_alignBAM.cpp ReadAlign_assignAlignToWindow.cpp ReadAlign_chimericDetection.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlign_mapOneRead.cpp ReadAlign_maxMappableLength2strands.cpp ReadAlign_multMapSelect.cpp ReadAlign_oneRead.cpp ReadAlign_outputAlignments.cpp ReadAlign_outputTranscriptCIGARp.cpp ReadAlign_outputTranscriptSAM.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_stitchPieces.cpp ReadAlign_stitchWindowSeeds.cpp ReadAlign_storeAligns.cpp STAR.cpp SequenceFuns.cpp SharedMemory.cpp Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp funCompareUintAndSuffixes.cpp funCompareUintAndSuffixesMemcmp.cpp genomeGenerate.cpp genomeParametersWrite.cpp genomeSAindex.cpp genomeScanFastaFiles.cpp insertSeqSA.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbInsertJunctions.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp sortSuffixesBucket.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c parametersDefault.xxd >> Depend.list
>clang-10: [0;1;35mwarning: [0mtreating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated][0m
>clang-10: [0;1;35mwarning: [0mparametersDefault.xxd: 'linker' input unused [-Wunused-command-line-argument][0m
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SharedMemory.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' PackedArray.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SuffixArrayFuns.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' STAR.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Parameters.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' InOutStreams.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' SequenceFuns.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Genome.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Chain.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Stats.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcript.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcript_alignScore.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_storeAligns.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_stitchPieces.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_multMapSelect.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_mapOneRead.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' readLoad.cpp
>SuffixArrayFuns.cpp:15:5: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>    register int64 ii;
>    ^~~~~~~~~
>SuffixArrayFuns.cpp:302:5: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>    register int64 ii;
>    ^~~~~~~~~
>SuffixArrayFuns.cpp:426:5: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>    register uint saind=0;
>    ^~~~~~~~~
>SuffixArrayFuns.cpp:429:9: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>        register uint128 g1=*( (uint128*) (G+SAstr) );
>        ^~~~~~~~~
>SuffixArrayFuns.cpp:432:13: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>            register char g2=(char) g1;
>            ^~~~~~~~~
>SuffixArrayFuns.cpp:446:9: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>        register uint128 g1=*( (uint128*) (G+P->nGenome-SAstr-16) );
>        ^~~~~~~~~
>SuffixArrayFuns.cpp:449:13: warning: 'register' storage class specifier is
>      deprecated and incompatible with C++17 [-Wdeprecated-register]
>            register char g2=(char) (g1>>(8*(15-ii)));
>            ^~~~~~~~~
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk_processChunks.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlignChunk_mapChunk.cpp
>7 warnings generated.
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' OutSJ.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' outputSJ.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' blocksOverlap.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ThreadControl.cpp
>STAR.cpp:416:23: warning: implicit conversion from 'double' to 'unsigned int'
>      changes value from 0.1 to 0 [-Wliteral-conversion]
>                sleep(0.1);
>                ~~~~~ ^~~
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sysRemoveDir.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_maxMappableLength2strands.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' binarySearch2.cpp
>sysRemoveDir.cpp:7:58: warning: unused parameter 'sb' [-Wunused-parameter]
>int removeFileOrDir(const char *fpath,const struct stat *sb, int typefla...
>                                                         ^
>sysRemoveDir.cpp:7:88: warning: unused parameter 'ftwbuf' [-Wunused-parameter]
>  ...char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
>                                                                  ^
>2 warnings generated.
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputAlignments.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptSAM.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptSJ.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_outputTranscriptCIGARp.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_createExtendWindowsWithAlign.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_assignAlignToWindow.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_oneRead.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_stitchWindowSeeds.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ReadAlign_chimericDetection.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stitchWindowAligns.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' extendAlign.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stitchAlignToTranscript.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' alignSmithWaterman.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeGenerate.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeParametersWrite.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeScanFastaFiles.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' genomeSAindex.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Genome_insertSequences.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' insertSeqSA.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' funCompareUintAndSuffixes.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' sortSuffixesBucket.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' funCompareUintAndSuffixesMemcmp.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' TimeFunctions.cpp
>funCompareUintAndSuffixesMemcmp.cpp:21:15: warning: unused variable 'p5'
>      [-Wunused-variable]
>        char *p5=g_funCompareUintAndSuffixesMemcmp_G+va[1]+g_funCompareU...
>              ^
>1 warning generated.
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' ErrorWarning.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' loadGTF.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' streamFuns.cpp
>x86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' stringSubstituteAll.cpp
>sortSuffixesBucket.cpp:27:40: error: arithmetic on a pointer to void
>        uint64_t iprev=*(uint64_t*)(ind+0*indSkip);
>                                    ~~~^
>sortSuffixesBucket.cpp:31:33: error: arithmetic on a pointer to void
>            if (*(uint64_t*)(ind+id*indSkip)==iprev)
>                             ~~~^
>sortSuffixesBucket.cpp:43:39: error: arithmetic on a pointer to void
>                iprev=*(uint64_t*)(ind+id*indSkip);
>                                   ~~~^
>sortSuffixesBucket.cpp:62:45: error: arithmetic on a pointer to void
>                charCount[G[*(uint64_t*)(ind+id*indSkip+8) + charShift]]...
>                                         ~~~^
>sortSuffixesBucket.cpp:85:46: error: arithmetic on a pointer tox86_64-pc-linux-gnu-clang++ -c  -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wall -Wextra -pthread `x86_64-pc-linux-gnu-pkg-config --cflags htslib` `x86_64-pc-linux-gnu-pkg-config --cflags zlib` -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="Tue Sep 8 10:47:07 CEST 2020 :/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source"' Transcriptome.cpp
> void
>                    char c=G[*(uint64_t*)(ind+id*indSkip+8) + charShift];
>                                          ~~~^
>sortSuffixesBucket.cpp:86:42: warning: array subscript is of type 'char'
>      [-Wchar-subscripts]
>                    memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip);
>                                         ^~
>sortSuffixesBucket.cpp:86:58: error: arithmetic on a pointer to void
>                    memcpy(ind1+charStart[c]*indSkip, ind+id*indSkip, indSkip);
>                                                      ~~~^
>sortSuffixesBucket.cpp:87:30: warning: array subscript is of type 'char'
>      [-Wchar-subscripts]
>                    charStart[c]++;
>                             ^~
>sortSuffixesBucket.cpp:89:27: error: arithmetic on a pointer to void
>                memcpy(ind+uB1[iu]*indSkip, ind1+uB1[iu]*indSkip, (uB2[i...
>                       ~~~^
>2 warnings and 7 errors generated.
>make: *** [Makefile:45: sortSuffixesBucket.o] Error 1
>make: *** Waiting for unfinished jobs....
>1 warning generated.
>make: Leaving directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source'
> * ERROR: sci-biology/STAR-2.5.3a::gentoo failed (compile phase):
> *   emake failed
> * 
> * If you need support, post the output of `emerge --info '=sci-biology/STAR-2.5.3a::gentoo'`,
> * the complete build log and the output of `emerge -pqv '=sci-biology/STAR-2.5.3a::gentoo'`.
> * The complete build log is located at '/var/log/emerge-log/build/sci-biology/STAR-2.5.3a:20200908-084659.log'.
> * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/STAR-2.5.3a/temp/build.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/STAR-2.5.3a/temp/environment'.
> * Working directory: '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a'
> * S: '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a'

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Attachments on bug 741152: 659126