Installing STAR on Mac: missing omp.h file
Ava Tg
I'm trying to install STAR on Mac OSX. My first attempt wan't successful. omp.h was missing in the package so I got this:
make STARforMacStatic
./IncludeDefine.h:22:10: fatal error: 'omp.h' file not found
#include <omp.h>
^
1 error generated.
Then found omp.h in https://github.com/alexdobin/STAR/tree/master/source/Mac_Include and copied over source directory but still couldn't install the package. This is the error message I get now:
./omp.h:280:1244: warning: missing terminating '"' character [-Winvalid-pp-token]
.../></div><button class="btn-link js-clone-selector" data-protocol="subversion" type="submit">Subversion</button></form>.
^
./omp.h:1031:28: warning: missing terminating ' character [-Winvalid-pp-token]
<!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><inpu...
^
4 warnings and 14 errors generated.
In file included from streamFuns.cpp:1:
In file included from ./streamFuns.h:4:
In file included from ./Parameters.h:4:
./IncludeDefine.h:22:10: error: 'omp.h' file not found with <angled> include; use "quotes" instead
#include <omp.h>
^~~~~~~
"omp.h"
In file included from streamFuns.cpp:1:
In file included from ./streamFuns.h:4:
In file included from ./Parameters.h:4:
In file included from ./IncludeDefine.h:22:
./omp.h:50:30: warning: missing terminating ' character [-Winvalid-pp-token]
<!-- </textarea> --><!-- '"` --><meta content="authenticity_token" name="csrf-param" />
^
./omp.h:95:32: warning: missing terminating ' character [-Winvalid-pp-token]
<!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/alexdobin/STAR/search" class="js-site-search-form" data-global-search-url="/search" data-re...
^
./omp.h:280:686: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...class="btn-link js-clone-selector" data-protocol="http" type="submit">HTTPS</button></form> or <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/us...
^
./omp.h:280:782: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...or <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/users/set_protocol?protocol_selector=subversion&protocol_type=clone" class="inline-form js...
^
./omp.h:280:891: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...class="inline-form js-clone-selector-form " data-form-nonce="870a386802fef917818bac79b516b26c5524c5b5" data-remote="true" method="post"><div style="margin:0;padding:0;...
^
./omp.h:280:905: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...class="inline-form js-clone-selector-form " data-form-nonce="870a386802fef917818bac79b516b26c5524c5b5" data-remote="true" method="post"><div style="margin:0;padding:0;...
^
./omp.h:280:923: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...class="inline-form js-clone-selector-form " data-form-nonce="870a386802fef917818bac79b516b26c5524c5b5" data-remote="true" method="post"><div style="margin:0;padding:0;...
^
./omp.h:280:971: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
..." data-form-nonce="870a386802fef917818bac79b516b26c5524c5b5" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="h...
^
./omp.h:280:983: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" ty...
^
./omp.h:280:1023: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" ty...
^
./omp.h:280:1049: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="...
^
./omp.h:280:1064: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="iI5s7NuZQenY/XELNTT...
^
./omp.h:280:1177: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
...name="authenticity_token" type="hidden" value="iI5s7NuZQenY/XELNTTzx4mjAXBUQSj+LqaxODSk1Y6w1g0m8Fdb+0Tk9qYY44wsP2MZFADksGbQM43Xh/ZU2w==" /></div><button class="btn-lin...
^
./omp.h:280:1220: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
.../></div><button class="btn-link js-clone-selector" data-protocol="subversion" type="submit">Subversion</button></form>.
^
./omp.h:280:1238: error: invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]
.../></div><button class="btn-link js-clone-selector" data-protocol="subversion" type="submit">Subversion</button></form>.
^
./omp.h:280:1244: warning: missing terminating '"' character [-Winvalid-pp-token]
.../></div><button class="btn-link js-clone-selector" data-protocol="subversion" type="submit">Subversion</button></form>.
^
./omp.h:1031:28: warning: missing terminating ' character [-Winvalid-pp-token]
<!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><inpu...
^
4 warnings and 14 errors generated.
make: *** [Depend.list] Error 1
I'm guessing I've got the wrong omp.h and would appreciate if you point me at right omp.h
Thanks for all the help,
Ava
Alexander Dobin
Ava Tg
Thanks for your reply. OMP libraries are now installed, but clang is still not happy!
clang: error: unsupported option '-static-libgcc'
make: *** [STARforMacStatic] Error 1
Shall I configure clang?
Thanks,
Avazeh
Alexander Dobin
Ava Tg
Sorry to reply late, was swamped by other tasks. Sure, let's do it.
make STARforMacStatic
Makefile:69: Depend.list: No such file or directory
xxd -i parametersDefault > parametersDefault.xxd
/Applications/Xcode.app/Contents/Developer/usr/bin/make -C htslib lib-static
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o bgzf.o bgzf.c
bgzf.c:68:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
KHASH_MAP_INIT_INT64(cache, cache_t)
^
./htslib/khash.h:599:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:7:1: note: expanded from here
kh_clear_cache
^
1 warning generated.
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o faidx.o faidx.c
faidx.c:21:1: warning: unused function 'kh_clear_s' [-Wunused-function]
KHASH_MAP_INIT_STR(s, faidx1_t)
^
./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:257:1: note: expanded from here
kh_clear_s
^
faidx.c:21:1: warning: unused function 'kh_del_s' [-Wunused-function]
./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:339:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:271:1: note: expanded from here
kh_del_s
^
2 warnings generated.
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "0.0.1"' > version.h
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c
hts.c:19:5: warning: unused function 'ks_getc' [-Wunused-function]
KSTREAM_INIT2(, BGZF*, bgzf_read, 65536)
^
./htslib/kseq.h:152:2: note: expanded from macro 'KSTREAM_INIT2'
__KS_INLINED(__read)
^
./htslib/kseq.h:68:20: note: expanded from macro '__KS_INLINED'
static inline int ks_getc(kstream_t *ks) \
^
hts.c:448:1: warning: unused function 'kh_clear_bin' [-Wunused-function]
KHASH_MAP_INIT_INT(bin, bins_t)
^
./htslib/khash.h:584:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:17:1: note: expanded from here
kh_clear_bin
^
2 warnings generated.
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o sam.o sam.c
sam.c:1335:1: warning: unused function 'kh_clear_olap_hash' [-Wunused-function]
KHASH_MAP_INIT_STR(olap_hash, lbnode_t *)
^
./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:207:1: note: expanded from here
kh_clear_olap_hash
^
1 warning generated.
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcf.o vcf.c
vcf.c:15:1: warning: unused function 'kh_clear_vdict' [-Wunused-function]
KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
^
./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:213:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_clear_##name(kh_##name##_t *h) \
^
<scratch space>:251:1: note: expanded from here
kh_clear_vdict
^
vcf.c:15:1: warning: unused function 'kh_del_vdict' [-Wunused-function]
./htslib/khash.h:615:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
^
./htslib/khash.h:356:2: note: expanded from macro 'KHASH_INIT'
KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:353:2: note: expanded from macro 'KHASH_INIT2'
__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
^
./htslib/khash.h:339:13: note: expanded from macro '__KHASH_IMPL'
SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
^
<scratch space>:265:1: note: expanded from here
kh_del_vdict
^
2 warnings generated.
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c
gcc -g -Wall -O2 -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
echo BAMbinSortByCoordinate.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.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 Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCounts.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp genomeGenerate.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
BAMbinSortByCoordinate.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.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 Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCounts.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp genomeGenerate.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
/bin/rm -f ./Depend.list
g++ -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:27 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' -MM BAMbinSortByCoordinate.cpp BAMfunctions.cpp BAMoutput.cpp ErrorWarning.cpp Genome.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 Stats.cpp SuffixArrayFuns.cpp ThreadControl.cpp TimeFunctions.cpp Transcript.cpp Transcript_alignScore.cpp Transcriptome.cpp Transcriptome_geneCounts.cpp Transcriptome_geneCountsAddAlign.cpp Transcriptome_quantAlign.cpp alignSmithWaterman.cpp bamRemoveDuplicates.cpp binarySearch2.cpp blocksOverlap.cpp extendAlign.cpp genomeGenerate.cpp loadGTF.cpp mapThreadsSpawn.cpp outputSJ.cpp readLoad.cpp serviceFuns.cpp signalFromBAM.cpp sjSplitAlign.cpp sjdbBuildIndex.cpp sjdbLoadFromFiles.cpp sjdbLoadFromStream.cpp sjdbPrepare.cpp stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
clang: warning: parametersDefault.xxd: 'linker' input unused
clang: warning: htslib: 'linker' input unused
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' PackedArray.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' SuffixArrayFuns.cpp
SuffixArrayFuns.cpp:15:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int64 ii;
^~~~~~~~~
SuffixArrayFuns.cpp:172:9: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int64 ii;
^~~~~~~~~
SuffixArrayFuns.cpp:143:82: warning: unused parameter 'dirR' [-Wunused-parameter]
uint suffixArraySearch(char** s2, uint S, uint N, char* G, PackedArray& SA, bool dirR, uint i1, uint i2, uint L, Parameters* P) {
^
3 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' STAR.cpp
STAR.cpp:306:23: warning: implicit conversion from 'double' to 'unsigned int' changes value from 0.1 to 0 [-Wliteral-conversion]
sleep(0.1);
~~~~~ ^~~
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Parameters.cpp
Parameters.cpp:718:21: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
for (int ii=0;ii<vAttr1.size();ii++) {
~~^~~~~~~~~~~~~~
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' InOutStreams.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' SequenceFuns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Genome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Stats.cpp
Stats.cpp:95:58: warning: unused parameter 'P' [-Wunused-parameter]
void Stats::reportFinal(ofstream &streamOut, Parameters *P) {
^
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcript.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcript_alignScore.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_storeAligns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_stitchPieces.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_multMapSelect.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_mapOneRead.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' readLoad.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk_processChunks.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk_mapChunk.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' OutSJ.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' outputSJ.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' blocksOverlap.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ThreadControl.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sysRemoveDir.cpp
sysRemoveDir.cpp:7:58: warning: unused parameter 'sb' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
sysRemoveDir.cpp:7:88: warning: unused parameter 'ftwbuf' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_maxMappableLength2strands.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' binarySearch2.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputAlignments.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputTranscriptSAM.cpp
ReadAlign_outputTranscriptSAM.cpp:246:25: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
for (int ii=0;ii<P->outSAMattrOrder.size();ii++) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputTranscriptSJ.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputTranscriptCIGARp.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_createExtendWindowsWithAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_assignAlignToWindow.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_oneRead.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_stitchWindowSeeds.cpp
ReadAlign_stitchWindowSeeds.cpp:114:18: warning: unused variable 'iS1' [-Wunused-variable]
uint iS1=seedChain[seedN-1];
^
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_chimericDetection.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stitchWindowAligns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' extendAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stitchAlignToTranscript.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' alignSmithWaterman.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' genomeGenerate.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' TimeFunctions.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ErrorWarning.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' loadGTF.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' streamFuns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stringSubstituteAll.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome_quantAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_quantTranscriptome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Quantifications.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome_geneCountsAddAlign.cpp
Transcriptome_geneCountsAddAlign.cpp:16:20: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare]
if (ib==a.nExons-1) {//binary search for the first time
~~^ ~~~~~~~~~~
Transcriptome_geneCountsAddAlign.cpp:27:34: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
} else if (gene1!=exG.g[e1]) {//another gene overlaps this read
~~~~~^ ~~~~~~~~~
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbLoadFromFiles.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbLoadFromStream.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbPrepare.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbBuildIndex.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' mapThreadsSpawn.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' BAMoutput.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' BAMfunctions.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_alignBAM.cpp
ReadAlign_alignBAM.cpp:92:15: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
if (x >= -127) {
~ ^ ~~~~
ReadAlign_alignBAM.cpp:186:20: note: in instantiation of function template specialization 'bamAttrArrayWriteInt<unsigned long long>' requested here
attrN+=bamAttrArrayWriteInt(trBest->nMM,"nM",attrOutArray+attrN,P);
^
ReadAlign_alignBAM.cpp:94:22: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
} else if (x >= -32767) {
~ ^ ~~~~~~
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' BAMbinSortByCoordinate.cpp
BAMbinSortByCoordinate.cpp:6:104: warning: unused parameter 'bgzfBAM' [-Wunused-parameter]
void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) {
^
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' signalFromBAM.cpp
signalFromBAM.cpp:63:30: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
for (uint32_t is=0;is<sigN;is++) {//formatting double output
~~^~~~~
signalFromBAM.cpp:81:38: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
for (uint32_t is=0;is<sigN;is++) {
~~^~~~~
signalFromBAM.cpp:86:43: warning: variable 'chrLen' is uninitialized when used here [-Wuninitialized]
for (uint32_t ig=0;ig<chrLen;ig++) {
^~~~~~
signalFromBAM.cpp:77:24: note: initialize the variable 'chrLen' to silence this warning
uint32_t chrLen;
^
= 0
3 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' bamRemoveDuplicates.cpp
bamRemoveDuplicates.cpp:23:25: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (int ii=0;ii<la;ii++) {
~~^~~
bamRemoveDuplicates.cpp:106:18: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (; ii<pa2[5]; ii+=2) {
~~^~~~~~~
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' bam_cat.c
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
g++ -o STAR -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:54:39 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' -pthread -lz -static-libgcc htslib/libhts.a PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o bam_cat.o
clang: error: unsupported option '-static-libgcc'
make: *** [STARforMacStatic] Error 1
at739-macair:source avazeh$ STAR --help
-bash: STAR: command not found
at739-macair:source avazeh$ make
g++ -o STAR -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 17:59:27 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o bam_cat.o -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
ld: warning: directory not found for option '-L/install/prefix/lib'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [STAR] Error 1
Ava Tg
I Also tried specifying clang as compiler but got the same error:
CXX=clang++ make
g++ -o STAR -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 18:33:33 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o bam_cat.o -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
ld: warning: directory not found for option '-L/install/prefix/lib'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [STAR] Error 1
CXX=clang++ make STARforMacStatic
g++ -o STAR -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 11 Aug 2015 18:34:04 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' -pthread -lz -static-libgcc htslib/libhts.a PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o bam_cat.o
clang: error: unsupported option '-static-libgcc'
make: *** [STARforMacStatic] Error 1
Ava Tg
gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.3.0
Alexander Dobin
Ava Tg
For OMP for Clang I followed the instruction here: https://clang-omp.github.io/
Would you suggest other resources? I think I should've tested it ...
Oops, sorry! But STARforMac failed too, details below. Let me know if you'd like me to test something
make STARforMac
xxd -i parametersDefault > parametersDefault.xxd
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' PackedArray.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' SuffixArrayFuns.cpp
SuffixArrayFuns.cpp:15:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int64 ii;
^~~~~~~~~
SuffixArrayFuns.cpp:172:9: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register]
register int64 ii;
^~~~~~~~~
SuffixArrayFuns.cpp:143:82: warning: unused parameter 'dirR' [-Wunused-parameter]
uint suffixArraySearch(char** s2, uint S, uint N, char* G, PackedArray& SA, bool dirR, uint i1, uint i2, uint L, Parameters* P) {
^
3 warnings generated.
STAR.cpp:306:23: warning: implicit conversion from 'double' to 'unsigned int' changes value from 0.1 to 0 [-Wliteral-conversion]
sleep(0.1);
~~~~~ ^~~
1 warning generated.
Parameters.cpp:718:21: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
for (int ii=0;ii<vAttr1.size();ii++) {
~~^~~~~~~~~~~~~~
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' SequenceFuns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Genome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Stats.cpp
Stats.cpp:95:58: warning: unused parameter 'P' [-Wunused-parameter]
void Stats::reportFinal(ofstream &streamOut, Parameters *P) {
^
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcript_alignScore.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_storeAligns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_stitchPieces.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_multMapSelect.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_mapOneRead.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' readLoad.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk_processChunks.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlignChunk_mapChunk.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' OutSJ.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' outputSJ.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' blocksOverlap.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ThreadControl.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sysRemoveDir.cpp
sysRemoveDir.cpp:7:58: warning: unused parameter 'sb' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
sysRemoveDir.cpp:7:88: warning: unused parameter 'ftwbuf' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' binarySearch2.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputAlignments.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputTranscriptSAM.cpp
ReadAlign_outputTranscriptSAM.cpp:246:25: warning: comparison of integers of different signs: 'int' and 'size_type' (aka 'unsigned long') [-Wsign-compare]
for (int ii=0;ii<P->outSAMattrOrder.size();ii++) {
~~^~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_outputTranscriptCIGARp.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_createExtendWindowsWithAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_assignAlignToWindow.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_oneRead.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_stitchWindowSeeds.cpp
ReadAlign_stitchWindowSeeds.cpp:114:18: warning: unused variable 'iS1' [-Wunused-variable]
uint iS1=seedChain[seedN-1];
^
1 warning generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stitchWindowAligns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' extendAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stitchAlignToTranscript.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' alignSmithWaterman.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' genomeGenerate.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' TimeFunctions.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ErrorWarning.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' loadGTF.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' streamFuns.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' stringSubstituteAll.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome_quantAlign.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_quantTranscriptome.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Quantifications.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' Transcriptome_geneCountsAddAlign.cpp
Transcriptome_geneCountsAddAlign.cpp:16:20: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare]
if (ib==a.nExons-1) {//binary search for the first time
~~^ ~~~~~~~~~~
Transcriptome_geneCountsAddAlign.cpp:27:34: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
} else if (gene1!=exG.g[e1]) {//another gene overlaps this read
~~~~~^ ~~~~~~~~~
2 warnings generated.
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbLoadFromStream.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbPrepare.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' sjdbBuildIndex.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' mapThreadsSpawn.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' BAMoutput.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' BAMfunctions.cpp
g++ -c -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 14 Aug 2015 18:22:06 BST :/Users/avazeh/projects/ribomap/prerequisites/STAR-STAR_2.4.0j/source"' ReadAlign_alignBAM.cpp
ReadAlign_alignBAM.cpp:92:15: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
if (x >= -127) {
~ ^ ~~~~
ReadAlign_alignBAM.cpp:186:20: note: in instantiation of function template specialization 'bamAttrArrayWriteInt<unsigned long long>' requested here
attrN+=bamAttrArrayWriteInt(trBest->nMM,"nM",attrOutArray+attrN,P);
^
ReadAlign_alignBAM.cpp:94:22: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
} else if (x >= -32767) {
~ ^ ~~~~~~
2 warnings generated.
BAMbinSortByCoordinate.cpp:6:104: warning: unused parameter 'bgzfBAM' [-Wunused-parameter]
void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) {
^
1 warning generated.
signalFromBAM.cpp:63:30: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
for (uint32_t is=0;is<sigN;is++) {//formatting double output
~~^~~~~
signalFromBAM.cpp:81:38: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
for (uint32_t is=0;is<sigN;is++) {
~~^~~~~
signalFromBAM.cpp:86:43: warning: variable 'chrLen' is uninitialized when used here [-Wuninitialized]
for (uint32_t ig=0;ig<chrLen;ig++) {
^~~~~~
signalFromBAM.cpp:77:24: note: initialize the variable 'chrLen' to silence this warning
uint32_t chrLen;
^
= 0
3 warnings generated.
bamRemoveDuplicates.cpp:23:25: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (int ii=0;ii<la;ii++) {
~~^~~
bamRemoveDuplicates.cpp:106:18: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (; ii<pa2[5]; ii+=2) {
~~^~~~~~~
2 warnings generated.
clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated
clang: error: no such file or directory: 'htslib/libhts.a'
make: *** [STARforMac] Error 1
Alexander Dobin
...
Mesude Bicak
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -o STAR -D'COMPILE_FOR_MAC' -I ./Mac_Include/ -O3 -pipe -std=c++0x -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue 29 Dec 2015 17:47:29 GMT :/Users/Mes/STAR-STAR_2.4.2a/source"' -pthread -lz htslib/libhts.a SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o
Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()':
Parameters_openReadsFiles.cpp:30:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
for (uint imate=0;imate<readNmates;imate++) {//open readIn files
^
Undefined symbols for architecture x86_64:
"exitWithError(std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_ostream<char, std::char_traits<char> >&, std::basic_ostream<char, std::char_traits<char> >&, int, Parameters&)", referenced from:
Parameters::openReadsFiles() in ccroumGe.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::copy(char*, unsigned long, unsigned long) const", referenced from:
genomeScanFastaFiles(Parameters*, char*, bool) in genomeGenerate.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::compare(char const*) const", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
Genome::freeMemory() in Genome.o
Genome::genomeLoad() in Genome.o
ReadAlign::multMapSelect() in ReadAlign_multMapSelect.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::compare(unsigned long, unsigned long, char const*, unsigned long) const", referenced from:
signalFromBAM(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters) in signalFromBAM.o
"std::__1::__vector_base_common<true>::__throw_length_error() const", referenced from:
__ZNSt3__16vectorIP17ParameterInfoBaseNS_9allocatorIS2_EEE6assignIPS2_EENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIS2_NS_15iterator_traitsIS9_E9referenceEEE5valueEvE4typeES9_S9_ in STAR.o
__ZNSt3__16vectorINS_12basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEENS4_IS6_EEE6assignIPS6_EENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIS6_NS_15iterator_traitsISC_E9referenceEEE5valueEvE4typeESC_SC_ in STAR.o
__ZNSt3__16vectorIyNS_9allocatorIyEEE6assignIPyEENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIyNS_15iterator_traitsIS7_E9referenceEEE5valueEvE4typeES7_S7_ in STAR.o
__ZNSt3__16vectorINS0_INS_12basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEENS4_IS6_EEEENS4_IS8_EEE6assignIPS8_EENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIS8_NS_15iterator_traitsISE_E9referenceEEE5valueEvE4typeESE_SE_ in STAR.o
std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >::vector(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&) in STAR.o
__ZNSt3__16vectorIdNS_9allocatorIdEEE6assignIPdEENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIdNS_15iterator_traitsIS7_E9referenceEEE5valueEvE4typeES7_S7_ in STAR.o
__ZNSt3__16vectorIiNS_9allocatorIiEEE6assignIPiEENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIiNS_15iterator_traitsIS7_E9referenceEEE5valueEvE4typeES7_S7_ in STAR.o
...
"std::__1::__vector_base_common<true>::__throw_out_of_range() const", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
ParameterInfoVector<unsigned long long>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<int>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<double>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
...
"std::__1::__basic_string_common<true>::__throw_length_error() const", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in STAR.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in Parameters.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in Genome.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in ReadAlign_storeAligns.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in ReadAlign_multMapSelect.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in readLoad.o
...
"std::__1::locale::has_facet(std::__1::locale::id&) const", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in InOutStreams.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in Genome.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in ReadAlign.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in ReadAlignChunk.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in outputSJ.o
...
"std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
_main in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
...
"std::__1::ios_base::getloc() const", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
_main in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanAllLines(std::__1::basic_istream<char, std::__1::char_traits<char> >&, int, int) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::at(unsigned long)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
ReadAlign::alignBAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::vector<int, std::__1::allocator<int> >, char**, unsigned long long*) in ReadAlign_alignBAM.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::erase(unsigned long, unsigned long)", referenced from:
genomeGenerate(Parameters*) in genomeGenerate.o
timeMonthDayTime() in TimeFunctions.o
timeMonthDayTime(long&) in TimeFunctions.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long)", referenced from:
_main in STAR.o
Parameters::Parameters() in Parameters.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
ParameterInfoVector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoScalar<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
Genome::genomeLoad() in Genome.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(char const*, unsigned long, unsigned long)", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
Genome::genomeLoad() in Genome.o
ReadAlignChunk::ReadAlignChunk(Parameters*, Genome&, Transcriptome*, int) in ReadAlignChunk.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(unsigned long, char)", referenced from:
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in SharedMemory.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in STAR.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in Parameters.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in Genome.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in Stats.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in ReadAlign.o
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in ReadAlign_storeAligns.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::append(char const*)", referenced from:
_main in STAR.o
ReadAlign::outputTranscriptSAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in ReadAlign_outputTranscriptSAM.o
BAMoutput::coordUnmappedPrepareBySJout() in BAMoutput.o
ReadAlign::samAttrNM_MD(Transcript const&, unsigned long long, unsigned long long, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in ReadAlign_alignBAM.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
signalFromBAM(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters) in signalFromBAM.o
BAMbinSortUnmapped(unsigned int, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortUnmapped.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::append(char const*, unsigned long)", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
Genome::genomeLoad() in Genome.o
ReadAlignChunk::ReadAlignChunk(Parameters*, Genome&, Transcriptome*, int) in ReadAlignChunk.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::assign(char const*)", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
ReadAlign::outputTranscriptSAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in ReadAlign_outputTranscriptSAM.o
genomeGenerate(Parameters*) in genomeGenerate.o
ReadAlign::samAttrNM_MD(Transcript const&, unsigned long long, unsigned long long, unsigned long long&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in ReadAlign_alignBAM.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::insert(std::__1::__wrap_iter<char const*>, char)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::insert(unsigned long, char const*)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
bamRemoveDuplicates(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in bamRemoveDuplicates.o
BAMbinSortUnmapped(unsigned int, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortUnmapped.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::insert(unsigned long, char const*, unsigned long)", referenced from:
BAMoutput::BAMoutput(int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in BAMoutput.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
BAMbinSortUnmapped(unsigned int, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortUnmapped.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::resize(unsigned long, char)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in STAR.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in STAR.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in Parameters.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Parameters.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in Genome.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::replace(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
stringSubstituteAll(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in stringSubstituteAll.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::reserve(unsigned long)", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
ParameterInfoScalar<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ReadAlignChunk::mapChunk() in ReadAlignChunk_mapChunk.o
ReadAlign::outputTranscriptSAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in ReadAlign_outputTranscriptSAM.o
ReadAlign::outputTranscriptCIGARp(Transcript const&) in ReadAlign_outputTranscriptCIGARp.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::push_back(char)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in STAR.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in Parameters.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
_main in STAR.o
__ZNSt3__16vectorINS_12basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEENS4_IS6_EEE6assignIPS6_EENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIS6_NS_15iterator_traitsISC_E9referenceEEE5valueEvE4typeESC_SC_ in STAR.o
std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > >::vector(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > > > const&) in STAR.o
std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long> > >::__insert_multi(std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long> const&) in STAR.o
Parameters::Parameters(Parameters const&) in STAR.o
std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, void*>*, long> std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long> > >::__insert_unique<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, unsigned long long> const&>(std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, void*>*, long>, std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const, unsigned long long> const&) in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::basic_string(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long, std::__1::allocator<char> const&)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_string()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in SharedMemory.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator=(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in SharedMemory.o
_main in STAR.o
Parameters::operator=(Parameters const&) in STAR.o
__ZNSt3__16vectorINS_12basic_stringIcNS_11char_traitsIcEENS_9allocatorIcEEEENS4_IS6_EEE6assignIPS6_EENS_9enable_ifIXaasr21__is_forward_iteratorIT_EE5valuesr16is_constructibleIS6_NS_15iterator_traitsISC_E9referenceEEE5valueEvE4typeESC_SC_ in STAR.o
void std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__map_value_compare<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::less<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long> > >::__assign_multi<std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, void*>*, long> >(std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, void*>*, long>, std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long>, void*>*, long>) in STAR.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in STAR.o
Parameters::Parameters() in Parameters.o
...
"std::__1::basic_istream<char, std::__1::char_traits<char> >::get()", referenced from:
ParameterInfoVector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoScalar<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::peek()", referenced from:
ParameterInfoVector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoScalar<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
readLoad(std::__1::basic_istream<char, std::__1::char_traits<char> >&, Parameters*, unsigned long long, unsigned long long&, unsigned long long&, char*, char*, char*, char*, char*, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, char&) in readLoad.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::read(char*, long)", referenced from:
fstreamReadBig(std::__1::basic_ifstream<char, std::__1::char_traits<char> >&, char*, unsigned long long) in streamFuns.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
BAMbinSortUnmapped(unsigned int, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortUnmapped.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::seekg(long long, std::__1::ios_base::seekdir)", referenced from:
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
ReadAlignChunk::chunkFstreamCat(std::__1::basic_fstream<char, std::__1::char_traits<char> >&, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, bool, _opaque_pthread_mutex_t&) in ReadAlignChunk.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
ReadAlignChunk::mapChunk() in ReadAlignChunk_mapChunk.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::tellg()", referenced from:
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::ignore(long, int)", referenced from:
readLoad(std::__1::basic_istream<char, std::__1::char_traits<char> >&, Parameters*, unsigned long long, unsigned long long&, unsigned long long&, char*, char*, char*, char*, char*, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, char&) in readLoad.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
genomeScanFastaFiles(Parameters*, char*, bool) in genomeGenerate.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_istream<char, std::__1::char_traits<char> >&, bool)", referenced from:
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in STAR.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::ws<char, std::__1::char_traits<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, char*) in readLoad.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, char&) in readLoad.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in ReadAlignChunk_processChunks.o
...
"std::__1::basic_istream<char, std::__1::char_traits<char> >::getline(char*, long, char)", referenced from:
Parameters::chrInfoLoad() in Parameters.o
readLoad(std::__1::basic_istream<char, std::__1::char_traits<char> >&, Parameters*, unsigned long long, unsigned long long&, unsigned long long&, char*, char*, char*, char*, char*, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, char&) in readLoad.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Genome.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
...
"std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Genome.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
...
"std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
_main in STAR.o
std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in STAR.o
virtual thunk to std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in STAR.o
std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in STAR.o
virtual thunk to std::__1::basic_ifstream<char, std::__1::char_traits<char> >::~basic_ifstream() in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
...
"std::__1::basic_istream<char, std::__1::char_traits<char> >::operator>>(double&)", referenced from:
ParameterInfoScalar<double>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoVector<double>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::operator>>(int&)", referenced from:
ParameterInfoScalar<int>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoVector<int>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ReadAlignChunk::processChunks() in ReadAlignChunk_processChunks.o
Transcriptome::Transcriptome(Parameters*) in Transcriptome.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::operator>>(unsigned int&)", referenced from:
Transcriptome::Transcriptome(Parameters*) in Transcriptome.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::operator>>(unsigned short&)", referenced from:
ParameterInfoScalar<unsigned short>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
Genome::genomeLoad() in Genome.o
Transcriptome::Transcriptome(Parameters*) in Transcriptome.o
"std::__1::basic_istream<char, std::__1::char_traits<char> >::operator>>(unsigned long long&)", referenced from:
Parameters::chrInfoLoad() in Parameters.o
ParameterInfoScalar<unsigned long long>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
ParameterInfoVector<unsigned long long>::inputValues(std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
Genome::genomeLoad() in Genome.o
readLoad(std::__1::basic_istream<char, std::__1::char_traits<char> >&, Parameters*, unsigned long long, unsigned long long&, unsigned long long&, char*, char*, char*, char*, char*, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, char&) in readLoad.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
Transcriptome::Transcriptome(Parameters*) in Transcriptome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::put(char)", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
Genome::genomeLoad() in Genome.o
Genome::HandleSharedMemoryException(SharedMemoryException const&, unsigned long long) in Genome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::flush()", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
InOutStreams::~InOutStreams() in InOutStreams.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::write(char const*, long)", referenced from:
ReadAlignChunk::mapChunk() in ReadAlignChunk_mapChunk.o
fstreamWriteBig(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, char*, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in streamFuns.o
BAMoutput::coordOneAlign(char*, unsigned long long, unsigned long long) in BAMoutput.o
BAMoutput::coordFlush() in BAMoutput.o
BAMoutput::coordUnmappedPrepareBySJout() in BAMoutput.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_ostream<char, std::__1::char_traits<char> >&)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Parameters.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Genome.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Stats.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in ReadAlign.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in ReadAlign_storeAligns.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::~sentry()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Parameters.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Genome.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Stats.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in ReadAlign.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in ReadAlign_storeAligns.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
_main in STAR.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(std::__1::basic_streambuf<char, std::__1::char_traits<char> >*)", referenced from:
ReadAlignChunk::chunkFstreamCat(std::__1::basic_fstream<char, std::__1::char_traits<char> >&, std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, bool, _opaque_pthread_mutex_t&) in ReadAlignChunk.o
ReadAlignChunk::chunkFilesCat(std::__1::basic_ostream<char, std::__1::char_traits<char> >*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, unsigned long long&) in ReadAlignChunk.o
copyFile(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in streamFuns.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(bool)", referenced from:
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
Genome::genomeLoad() in Genome.o
fstreamWriteBig(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, char*, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in streamFuns.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(double)", referenced from:
ParameterInfoScalar<double>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<double>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
Stats::progressReport(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&) in Stats.o
Stats::reportFinal(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, Parameters*) in Stats.o
signalFromBAM(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters) in signalFromBAM.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(int)", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
Parameters::inputParameters(int, char**) in Parameters.o
ParameterInfoScalar<int>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<int>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
Genome::genomeLoad() in Genome.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned int)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
Junction::collapseOneSJ(char*, char*, Parameters*) in OutSJ.o
Junction::outputStream(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, Parameters*) in OutSJ.o
Transcriptome::Transcriptome(Parameters*) in Transcriptome.o
BAMoutput::coordBins() in BAMoutput.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
signalFromBAM(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters) in signalFromBAM.o
...
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(long)", referenced from:
readLoad(std::__1::basic_istream<char, std::__1::char_traits<char> >&, Parameters*, unsigned long long, unsigned long long&, unsigned long long&, char*, char*, char*, char*, char*, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, unsigned long long&, char&) in readLoad.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned long)", referenced from:
genomeScanFastaFiles(Parameters*, char*, bool) in genomeGenerate.o
loadGTF(SjdbClass&, Parameters*, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >) in loadGTF.o
fstreamWriteBig(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, char*, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in streamFuns.o
Transcriptome::quantsOutput() in Transcriptome.o
sjdbLoadFromFiles(Parameters*, SjdbClass&) in sjdbLoadFromFiles.o
sjdbInsertJunctions(Parameters*, Parameters*, Genome&, SjdbClass&) in sjdbInsertJunctions.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned short)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
ParameterInfoScalar<unsigned short>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
Junction::outputStream(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, Parameters*) in OutSJ.o
ReadAlign::outputTranscriptSAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in ReadAlign_outputTranscriptSAM.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(long long)", referenced from:
fstreamWriteBig(std::__1::basic_ofstream<char, std::__1::char_traits<char> >&, char*, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in streamFuns.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(unsigned long long)", referenced from:
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
ParameterInfoScalar<unsigned long long>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
ParameterInfoVector<unsigned long long>::printValues(std::__1::basic_ostream<char, std::__1::char_traits<char> >&) const in Parameters.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
Genome::genomeLoad() in Genome.o
...
"std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
non-virtual thunk to std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
virtual thunk to std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
non-virtual thunk to std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
virtual thunk to std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringstream() in Parameters.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::sync()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_storeAligns.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_multMapSelect.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_storeAligns.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_multMapSelect.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::uflow()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in InOutStreams.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::setbuf(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_storeAligns.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in ReadAlign_multMapSelect.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsgetn(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in InOutStreams.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsputn(char const*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in InOutStreams.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::showmanyc()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in Parameters.o
vtable for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in InOutStreams.o
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::basic_streambuf()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
_main in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
...
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::~basic_streambuf()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in SharedMemory.o
...
"std::__1::cerr", referenced from:
SharedMemory::SharedMemory(int, bool) in SharedMemory.o
SharedMemory::SharedMemory(int, bool) in SharedMemory.o
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
Genome::OpenStream(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_ifstream<char, std::__1::char_traits<char> >&) in Genome.o
...
"std::__1::cout", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
"std::__1::ctype<char>::id", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
_main in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanAllLines(std::__1::basic_istream<char, std::__1::char_traits<char> >&, int, int) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
...
"std::__1::locale::locale(std::__1::locale const&)", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in InOutStreams.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in Genome.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in ReadAlign.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in ReadAlignChunk.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in outputSJ.o
...
"std::__1::locale::~locale()", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
_main in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanAllLines(std::__1::basic_istream<char, std::__1::char_traits<char> >&, int, int) in Parameters.o
...
"std::__1::codecvt<char, char, __mbstate_t>::id", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in InOutStreams.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::basic_filebuf() in InOutStreams.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&) in Genome.o
...
"std::__1::ios_base::__set_badbit_and_consider_rethrow()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in STAR.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::operator>><char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&) in Parameters.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::ws<char, std::__1::char_traits<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&) in Parameters.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in Parameters.o
...
"std::__1::ios_base::init(void*)", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
_main in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
InOutStreams::InOutStreams() in InOutStreams.o
...
"std::__1::ios_base::clear(unsigned int)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
_main in STAR.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in STAR.o
std::__1::basic_istream<char, std::__1::char_traits<char> >& std::__1::getline<char, std::__1::char_traits<char>, std::__1::allocator<char> >(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char) in STAR.o
Parameters::inputParameters(int, char**) in Parameters.o
Parameters::scanOneLine(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, int, int) in Parameters.o
Parameters::chrInfoLoad() in Parameters.o
...
"std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
_main in STAR.o
...
"std::__1::to_string(long long)", referenced from:
Parameters::inputParameters(int, char**) in Parameters.o
BAMbinSortByCoordinate(unsigned int, unsigned long long, unsigned long long, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortByCoordinate.o
bamRemoveDuplicates(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in bamRemoveDuplicates.o
BAMbinSortUnmapped(unsigned int, unsigned long long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, BGZF*, Parameters*) in BAMbinSortUnmapped.o
"std::__1::to_string(unsigned long long)", referenced from:
_main in STAR.o
ReadAlign::outputTranscriptSAM(Transcript const&, unsigned long long, unsigned long long, unsigned long long, unsigned long long, char, int, bool*, std::__1::basic_ostream<char, std::__1::char_traits<char> >*) in ReadAlign_outputTranscriptSAM.o
ReadAlign::chimericDetection() in ReadAlign_chimericDetection.o
genomeGenerate(Parameters*) in genomeGenerate.o
BAMoutput::BAMoutput(int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, Parameters*) in BAMoutput.o
BAMoutput::coordUnmappedPrepareBySJout() in BAMoutput.o
bam_cigarString(bam1_t*) in BAMfunctions.o
...
"std::bad_cast::bad_cast()", referenced from:
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::overflow(int) in STAR.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::seekoff(long long, std::__1::ios_base::seekdir, unsigned int) in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::sync() in Parameters.o
std::__1::basic_filebuf<char, std::__1::char_traits<char> >::underflow() in Parameters.o
...
"typeinfo for std::__1::basic_istream<char, std::__1::char_traits<char> >", referenced from:
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
typeinfo for std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
typeinfo for std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
...
"typeinfo for std::__1::basic_ostream<char, std::__1::char_traits<char> >", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
typeinfo for std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
typeinfo for std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
typeinfo for std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
...
"typeinfo for std::__1::basic_iostream<char, std::__1::char_traits<char> >", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
typeinfo for std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
typeinfo for std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
typeinfo for std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"typeinfo for std::__1::basic_streambuf<char, std::__1::char_traits<char> >", referenced from:
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in STAR.o
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in Parameters.o
typeinfo for std::__1::basic_filebuf<char, std::__1::char_traits<char> > in InOutStreams.o
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"non-virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"non-virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Genome.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
...
"virtual thunk to std::__1::basic_istream<char, std::__1::char_traits<char> >::~basic_istream()", referenced from:
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_istringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_ifstream<char, std::__1::char_traits<char> > in Genome.o
construction vtable for std::__1::basic_istream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
...
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in STAR.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ofstream<char, std::__1::char_traits<char> > in InOutStreams.o
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Genome.o
...
"virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
"virtual thunk to std::__1::basic_iostream<char, std::__1::char_traits<char> >::~basic_iostream()", referenced from:
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in Parameters.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_fstream<char, std::__1::char_traits<char> > in ReadAlign.o
construction vtable for std::__1::basic_iostream<char, std::__1::char_traits<char> >-in-std::__1::basic_stringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in OutSJ.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [STARforMac] Error 1
I'd greatly appreciate if you could please help me out.
I heard and read great stuff about STAR and would love to have it working on my Mac!
Many thanks in advance,
Mesude
...
Alexander Dobin
Mesude Bicak
...
zhe zhang
[~] $ cd /Users/rabbit04/Desktop/software/STAR/source
[~/Desktop/software/STAR/source] $ make STARforMacStatic CXX=/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Tue Dec 29 15:49:10 PST 2015 :/Users/rabbit04/Desktop/software/STAR/source"' -D'COMPILE_FOR_MAC' SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp -pthread -lz -static-libgcc htslib/libhts.a
Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()':
Parameters_openReadsFiles.cpp:30:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
for (uint imate=0;imate<readNmates;imate++) {//open readIn files
^
Undefined symbols for architecture x86_64:
"std::__1::__basic_string_common<true>::__throw_length_error() const", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str() const in SharedMemory.o
"std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::ios_base::getloc() const", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::__init(unsigned long, char)", referenced from:
std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> > std::__1::__pad_and_output<char, std::__1::char_traits<char> >(std::__1::ostreambuf_iterator<char, std::__1::char_traits<char> >, char const*, char const*, char const*, std::__1::ios_base&, char) in SharedMemory.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::resize(unsigned long, char)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in SharedMemory.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::push_back(char)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::overflow(int) in SharedMemory.o
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_string()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in SharedMemory.o
...
"std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::operator=(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::str(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::put(char)", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::flush()", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::sentry(std::__1::basic_ostream<char, std::__1::char_traits<char> >&)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::sentry::~sentry()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
"std::__1::basic_ostream<char, std::__1::char_traits<char> >::operator<<(int)", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::sync()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::imbue(std::__1::locale const&)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::uflow()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::setbuf(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsgetn(char*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::xsputn(char const*, long)", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::showmanyc()", referenced from:
vtable for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::basic_streambuf()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
"std::__1::basic_streambuf<char, std::__1::char_traits<char> >::~basic_streambuf()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_stringbuf() in SharedMemory.o
...
"std::__1::cerr", referenced from:
SharedMemory::SharedMemory(int, bool) in SharedMemory.o
SharedMemory::SharedMemory(int, bool) in SharedMemory.o
"std::__1::ctype<char>::id", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::locale::~locale()", referenced from:
SharedMemory::~SharedMemory() in SharedMemory.o
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::ios_base::__set_badbit_and_consider_rethrow()", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::ios_base::init(void*)", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
"std::__1::ios_base::clear(unsigned int)", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits<char> >& std::__1::__put_character_sequence<char, std::__1::char_traits<char> >(std::__1::basic_ostream<char, std::__1::char_traits<char> >&, char const*, unsigned long) in SharedMemory.o
"std::__1::basic_ios<char, std::__1::char_traits<char> >::~basic_ios()", referenced from:
SharedMemory::GetPosixObjectKey() in SharedMemory.o
SharedMemory::CounterName() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
virtual thunk to std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >::~basic_ostringstream() in SharedMemory.o
"typeinfo for std::__1::basic_ostream<char, std::__1::char_traits<char> >", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
typeinfo for std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"typeinfo for std::__1::basic_streambuf<char, std::__1::char_traits<char> >", referenced from:
typeinfo for std::__1::basic_stringbuf<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
"virtual thunk to std::__1::basic_ostream<char, std::__1::char_traits<char> >::~basic_ostream()", referenced from:
construction vtable for std::__1::basic_ostream<char, std::__1::char_traits<char> >-in-std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> > in SharedMemory.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [STARforMacStatic] Error 1
...
Alexander Dobin
...
zhe zhang
inserting junctions into the genome indices. Is that common? Based on your experience, how long it normally take to build index?
Thanks a lot.
Zhe
Alexander Dobin
antonio ahn
1. brew install gcc49 (this installed at (/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9)
2. Install the latest STAR (2.5.1b)
3. cd to STAR source/ directory and run
make pointing to the installed gcc executable.
Run Command:
1. "make clean"
2. "make STARforMacStatic CXX=/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9"
This appears to work well at first however i get a error message at the end.
Could you please help me?
Thank you so much. I have pasted the error message underneath
Antonio
Antonios-MacBook-Air:source antonioahn$ make STARforMacStatic CXX=/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9
Makefile:91: Depend.list: No such file or directory
echo BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.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 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 stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.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 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 stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c
/bin/rm -f ./Depend.list
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:31 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -MM BAMbinSortByCoordinate.cpp BAMbinSortUnmapped.cpp BAMfunctions.cpp BAMoutput.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 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 stitchAlignToTranscript.cpp stitchGapIndel.cpp stitchWindowAligns.cpp streamFuns.cpp stringSubstituteAll.cpp sysRemoveDir.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list
g++-4.9: warning: parametersDefault.xxd: linker input file unused because linking not done
g++-4.9: warning: htslib: linker input file unused because linking not done
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' SharedMemory.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' PackedArray.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' SuffixArrayFuns.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' STAR.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Parameters.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' InOutStreams.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' SequenceFuns.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Genome.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Stats.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Transcript.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Transcript_alignScore.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_storeAligns.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_stitchPieces.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_multMapSelect.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_mapOneRead.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' readLoad.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlignChunk.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlignChunk_processChunks.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlignChunk_mapChunk.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' OutSJ.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' outputSJ.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' blocksOverlap.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ThreadControl.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sysRemoveDir.cpp
sysRemoveDir.cpp:7:58: warning: unused parameter 'sb' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
sysRemoveDir.cpp:7:88: warning: unused parameter 'ftwbuf' [-Wunused-parameter]
int removeFileOrDir(const char *fpath,const struct stat *sb, int typeflag, struct FTW *ftwbuf) {
^
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_maxMappableLength2strands.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' binarySearch2.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_outputAlignments.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_outputTranscriptSAM.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_outputTranscriptSJ.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_outputTranscriptCIGARp.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_createExtendWindowsWithAlign.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_assignAlignToWindow.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_oneRead.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_stitchWindowSeeds.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_chimericDetection.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' stitchWindowAligns.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' extendAlign.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' stitchAlignToTranscript.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' alignSmithWaterman.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' genomeGenerate.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' genomeParametersWrite.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' genomeScanFastaFiles.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' genomeSAindex.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Genome_insertSequences.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' insertSeqSA.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' funCompareUintAndSuffixes.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' TimeFunctions.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ErrorWarning.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' loadGTF.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' streamFuns.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' stringSubstituteAll.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Transcriptome.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Transcriptome_quantAlign.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_quantTranscriptome.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Quantifications.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' Transcriptome_geneCountsAddAlign.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sjdbLoadFromFiles.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sjdbLoadFromStream.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sjdbPrepare.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sjdbBuildIndex.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' sjdbInsertJunctions.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' mapThreadsSpawn.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' BAMoutput.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' BAMfunctions.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' ReadAlign_alignBAM.cpp
ReadAlign_alignBAM.cpp: In instantiation of 'int bamAttrArrayWriteInt(intType, const char*, char*, Parameters*) [with intType = long long unsigned int]':
ReadAlign_alignBAM.cpp:212:76: required from here
ReadAlign_alignBAM.cpp:92:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (x >= -127) {
^
ReadAlign_alignBAM.cpp:94:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
} else if (x >= -32767) {
^
ReadAlign_alignBAM.cpp:98:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (!(x>=-2147483647)) {
^
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' BAMbinSortByCoordinate.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' signalFromBAM.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' bamRemoveDuplicates.cpp
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' BAMbinSortUnmapped.cpp
BAMbinSortUnmapped.cpp:5:78: warning: unused parameter 'bgzfBAM' [-Wunused-parameter]
void BAMbinSortUnmapped(uint32 iBin, uint nThreads, string dirBAMsort, BGZF *bgzfBAM, Parameters *P) {
^
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -c -O3 -pipe -Wall -Wextra bam_cat.c
/usr/local/Cellar/gcc49/4.9.3/bin/g++-4.9 -o STAR -O3 -pipe -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Fri 1 Apr 2016 22:13:39 NZDT :/Users/antonioahn/Desktop/STAR-2.5.1b/source"' -D'COMPILE_FOR_MAC' SharedMemory.o PackedArray.o SuffixArrayFuns.o STAR.o Parameters.o InOutStreams.o SequenceFuns.o Genome.o Stats.o Transcript.o Transcript_alignScore.o ReadAlign.o ReadAlign_storeAligns.o ReadAlign_stitchPieces.o ReadAlign_multMapSelect.o ReadAlign_mapOneRead.o readLoad.o ReadAlignChunk.o ReadAlignChunk_processChunks.o ReadAlignChunk_mapChunk.o OutSJ.o outputSJ.o blocksOverlap.o ThreadControl.o sysRemoveDir.o ReadAlign_maxMappableLength2strands.o binarySearch2.o ReadAlign_outputAlignments.o ReadAlign_outputTranscriptSAM.o ReadAlign_outputTranscriptSJ.o ReadAlign_outputTranscriptCIGARp.o ReadAlign_createExtendWindowsWithAlign.o ReadAlign_assignAlignToWindow.o ReadAlign_oneRead.o ReadAlign_stitchWindowSeeds.o ReadAlign_chimericDetection.o stitchWindowAligns.o extendAlign.o stitchAlignToTranscript.o alignSmithWaterman.o genomeGenerate.o genomeParametersWrite.o genomeScanFastaFiles.o genomeSAindex.o Genome_insertSequences.o insertSeqSA.o funCompareUintAndSuffixes.o TimeFunctions.o ErrorWarning.o loadGTF.o streamFuns.o stringSubstituteAll.o Transcriptome.o Transcriptome_quantAlign.o ReadAlign_quantTranscriptome.o Quantifications.o Transcriptome_geneCountsAddAlign.o sjdbLoadFromFiles.o sjdbLoadFromStream.o sjdbPrepare.o sjdbBuildIndex.o sjdbInsertJunctions.o mapThreadsSpawn.o Parameters_openReadsFiles.cpp Parameters_closeReadsFiles.cpp BAMoutput.o BAMfunctions.o ReadAlign_alignBAM.o BAMbinSortByCoordinate.o signalFromBAM.o bamRemoveDuplicates.o BAMbinSortUnmapped.o bam_cat.o GlobalVariables.cpp -pthread -lz -static-libgcc htslib/libhts.a
Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()':
Parameters_openReadsFiles.cpp:30:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
for (uint imate=0;imate<readNmates;imate++) {//open readIn files
^
ld: warning: direct access in std::basic_ios<char, std::char_traits<char> >::fill() const to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ios<char, std::char_traits<char> >::fill(char) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ios<char, std::char_traits<char> >::widen(char) const to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ios<char, std::char_traits<char> >::copyfmt(std::basic_ios<char, std::char_traits<char> > const&) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ios<char, std::char_traits<char> >::copyfmt(std::basic_ios<char, std::char_traits<char> > const&) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_istream<char, std::char_traits<char> >::getline(char*, long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_istream<char, std::char_traits<char> >::get(char*, long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_istream<char, std::char_traits<char> >::get(std::basic_streambuf<char, std::char_traits<char> >&) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_istream<char, std::char_traits<char> >& std::operator>><char, std::char_traits<char> >(std::basic_istream<char, std::char_traits<char> >&, std::_Setfill<char>) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::ctype<char>::widen(char) const [clone .part.28] to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::time_put<char, std::ostreambuf_iterator<char, std::char_traits<char> > >::do_put(std::ostreambuf_iterator<char, std::char_traits<char> >, std::ios_base&, char, tm const*, char, char) const to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::__pad<char, std::char_traits<char> >::_S_pad(std::ios_base&, char, char*, char const*, long, long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_istream<char, std::char_traits<char> >& std::getline<char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >&) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::endl<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::operator<< <char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, std::_Setfill<char>) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<long>(long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<bool>(bool) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<long long>(long long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long long>(unsigned long long) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<double>(double) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<long double>(long double) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
ld: warning: direct access in std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<void const*>(void const*) to global weak symbol std::ctype<char>::do_widen(char) const means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
Alexander Dobin
antonio ahn
dn-wlan-171-181:source antonioahn$ pwd
/Users/antonioahn/Desktop/STAR-2.5.1b/source
dn-wlan-171-181:source antonioahn$ STAR
-bash: STAR: command not found
Thank you very much,
Antonio
...
Alexander Dobin
...
antonio ahn
$ ls -l STAR
-rwxr-xr-x 1 antonioahn staff 3448204 8 Apr 01:10 STAR
$ mkdir /Users/antonioahn/Desktop/STAR-2.5.1b/Run1
$ /Users/antonioahn/Desktop/STAR-2.5.1b/source/STAR --version
STAR_2.5.1b
Alexander Dobin
(if you cannot access it, I will send you PDF by e-mail).
...
antonio ahn
...
antonio ahn
...