You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     j...@freebsd.org
Last committer: ger...@freebsd.org
Ident:          $FreeBSD: head/biology/star/Makefile 507372 2019-07-26 
20:46:53Z gerald $
Log URL:        
http://beefy8.nyi.freebsd.org/data/head-armv6-default/p511388_s351963/logs/rna-STAR-2.7.0.f_1.log
Build URL:      
http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p511388_s351963
Log:

=>> Building biology/star
build started at Wed Sep 11 04:49:33 UTC 2019
port directory: /usr/ports/biology/star
package name: rna-STAR-2.7.0.f_1
building for: FreeBSD head-armv6-default-job-14 13.0-CURRENT FreeBSD 
13.0-CURRENT 1300046 arm
maintained by: j...@freebsd.org
Makefile ident:      $FreeBSD: head/biology/star/Makefile 507372 2019-07-26 
20:46:53Z gerald $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300031
Jail OSVERSION: 1300046
Job Id: 14




!!! Jail is newer than host. (Jail: 1300046, Host: 1300031) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   rna-STAR-2.7.0.f_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.11.1.txz
[head-armv6-default-job-14] Installing pkg-1.11.1...
[head-armv6-default-job-14] Extracting pkg-1.11.1: .......... done
===>   rna-STAR-2.7.0.f_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of rna-STAR-2.7.0.f_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
<snip>
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/cram_index.o cram/cram_index.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function 'paranoid_fclose':
cram/cram_io.c:1006:15: warning: implicit declaration of function 'fsync' 
[-Wimplicit-function-declaration]
 1006 |     if (-1 == fsync(fileno(fp))) {
      |               ^~~~~
cram/cram_io.c: In function 'refs_from_header':
cram/cram_io.c:1279:49: warning: unused parameter 'fd' [-Wunused-parameter]
 1279 | static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) {
      |                                        ~~~~~~~~~^~
In file included from ./cram/cram_io.h:52,
                 from ./cram/cram.h:55,
                 from cram/cram_io.c:65:
cram/cram_io.c: In function 'expand_cache_path':
./cram/misc.h:103:26: warning: comparison of integer expressions of different 
signedness: 'long int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                          ^
cram/cram_io.c:1368:10: note: in expansion of macro 'MIN'
 1368 |      l = MIN(l, strlen(fn));
      |          ^~~
./cram/misc.h:103:36: warning: operand of ?: changes signedness from 'long int' 
to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand 
[-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                                    ^~~
cram/cram_io.c:1368:10: note: in expansion of macro 'MIN'
 1368 |      l = MIN(l, strlen(fn));
      |          ^~~
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:1544:6: warning: implicit declaration of function 'unlink' 
[-Wimplicit-function-declaration]
 1544 |      unlink(path_tmp);
      |      ^~~~~~
cram/cram_io.c: In function 'full_path':
cram/cram_io.c:2915:7: warning: implicit declaration of function 'getcwd'; did 
you mean 'getw'? [-Wimplicit-function-declaration]
 2915 |  if (!getcwd(out, PATH_MAX) ||
      |       ^~~~~~
      |       getw
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:1529:27: warning: '.tmp_' directive writing 5 bytes into a 
region of size between 1 and 1024 [-Wformat-overflow=]
 1529 |      sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
      |                           ^~~~~
cram/cram_io.c:1529:24: note: directive argument in the range [0, 2147483647]
 1529 |      sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
      |                        ^~~~~~~~~~~
cram/cram_io.c:1529:6: note: 'sprintf' output between 7 and 1039 bytes into a 
destination of size 1024
 1529 |      sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
    inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:2987:3:
cram/cram_io.c:2917:6: warning: 'strncpy' specified bound 1024 equals 
destination size [-Wstringop-truncation]
 2917 |      strncpy(out, in, PATH_MAX);
      |      ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2909:2: warning: 'strncpy' specified bound 1024 equals 
destination size [-Wstringop-truncation]
 2909 |  strncpy(out, in, PATH_MAX);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c: In function 'cram_dopen':
cram/cram_io.c:3291:2: warning: 'strncpy' specified bound 20 equals destination 
size [-Wstringop-truncation]
 3291 |  strncpy(def.file_id, filename, 20);
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c
cram/cram_stats.c: In function 'cram_stats_add':
cram/cram_stats.c:74:6: warning: suggest braces around empty body in an 'else' 
statement [-Wempty-body]
   74 |      ; // FIXME: handle error
      |      ^
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/files.o cram/files.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c
cram/mFILE.c: In function 'mfload':
cram/mFILE.c:73:65: warning: unused parameter 'binary' [-Wunused-parameter]
   73 | static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) 
{
      |                                                             ~~~~^~~~~~
cram/mFILE.c: In function 'mftruncate':
cram/mFILE.c:416:31: warning: operand of ?: changes signedness from 'long int' 
to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand 
[-Wsign-compare]
  416 |     mf->size = offset != -1 ? offset : mf->offset;
      |                               ^~~~~~
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c
In file included from cram/open_trace_file.c:81:
cram/open_trace_file.c: In function 'find_file_dir':
./cram/misc.h:103:26: warning: comparison of integer expressions of different 
signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                          ^
cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN'
  271 |   path_end += MIN(strlen(file), l);
      |               ^~~
./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' 
to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand 
[-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                                          ^~~
cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN'
  271 |   path_end += MIN(strlen(file), l);
      |               ^~~
./cram/misc.h:103:26: warning: comparison of integer expressions of different 
signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                          ^
cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN'
  272 |   file     += MIN(strlen(file), l);
      |               ^~~
./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' 
to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand 
[-Wsign-compare]
  103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
      |                                          ^~~
cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN'
  272 |   file     += MIN(strlen(file), l);
      |               ^~~
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c
cram/sam_header.c: In function 'sam_hdr_add_lines':
cram/sam_header.c:320:9: warning: comparison of integer expressions of 
different signedness: 'int' and 'khint_t' {aka 'unsigned int'} [-Wsign-compare]
  320 |  if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new)))
      |         ^~
cram/sam_header.c: In function 'sam_hdr_vadd':
cram/sam_header.c:440:12: warning: comparison of integer expressions of 
different signedness: 'int' and 'khint32_t' {aka 'unsigned int'} 
[-Wsign-compare]
  440 |     if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new)))
      |            ^~
cram/sam_header.c: In function 'sam_hdr_find_key':
cram/sam_header.c:672:40: warning: unused parameter 'sh' [-Wunused-parameter]
  672 | SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh,
      |                               ~~~~~~~~~^~
cram/sam_header.c: In function 'sam_hdr_rebuild':
cram/sam_header.c:781:24: warning: comparison of integer expressions of 
different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' 
[-Wsign-compare]
  781 |  if (kh_key(hdr->h, k) == K("HD"))
      |                        ^~
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c
cram/vlen.c: In function 'vflen':
cram/vlen.c:121:9: warning: variable 'i' set but not used 
[-Wunused-but-set-variable]
  121 |     int i;
      |         ^
gcc9 -g -Wall -O2 -O2 -pipe  -fstack-protector-strong 
-Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing  -Wall -Wextra  -I. 
-DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o 
hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o 
cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o 
cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o 
cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o 
cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gmake[2]: Leaving directory 
'/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source/htslib'
echo ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp 
ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp 
loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp 
funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp 
ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp 
SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp 
ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp 
ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp 
streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp 
sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp 
serviceFuns.cpp ReadAlignChunk_mapChunk.cpp 
ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp 
ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp 
GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp 
ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSpli
 t.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp 
stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp 
Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp 
Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp 
blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp 
PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp 
SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp 
ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp 
Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp 
BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp 
STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp 
ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp 
Transcriptome_geneCountsAddAlign.cpp 
ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp 
Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.
 cpp ReadAlign_mapOneRead.cpp ReadAlign_outpu!
 tTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp 
genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp 
ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp 
ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp 
extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp 
Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp 
ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp 
SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp 
ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp 
ThreadControl.cpp Transcript.cpp bam_cat.c
ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp 
ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp 
loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp 
funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp 
ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp 
SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp 
ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp 
ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp 
streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp 
sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp 
serviceFuns.cpp ReadAlignChunk_mapChunk.cpp 
ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp 
ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp 
GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp 
ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp 
sjAlignSplit.cpp
  Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp 
stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp 
Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp 
Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp 
blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp 
PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp 
SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp 
ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp 
Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp 
BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp 
STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp 
ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp 
Transcriptome_geneCountsAddAlign.cpp 
ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp 
Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp R
 eadAlign_mapOneRead.cpp ReadAlign_outputTran!
 scriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp 
genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp 
ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp 
ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp 
extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp 
Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp 
ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp 
SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp 
ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp 
ThreadControl.cpp Transcript.cpp bam_cat.c
'rm' -f ./Depend.list
g++9 -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 11 
04:50:14 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-MM ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp 
ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp 
loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp 
funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp 
ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp 
SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp 
ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp 
ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp 
streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp 
sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp 
serviceFuns.cpp ReadAlignChunk_mapChunk.cpp 
ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp 
ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters
 .cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp 
ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp 
sjAlignSplit.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp 
stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp 
Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp 
Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp 
blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp 
PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp 
SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp 
ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp 
Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp 
BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp 
STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp 
ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp 
Transcriptome_geneCoun
 tsAddAlign.cpp ChimericDetection_chimericDet!
 ectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp 
ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp 
ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp 
Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp 
ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp 
ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp 
extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp 
Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp 
ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp 
SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp 
ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp 
ThreadControl.cpp Transcript.cpp bam_cat.c parametersDefault.xxd htslib >> 
Depend.list
g++9: warning: parametersDefault.xxd: linker input file unused because linking 
not done
g++9: warning: htslib: linker input file unused because linking not done
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  ParametersSolo.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloRead.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloRead_record.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloReadBarcode.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloReadBarcode_getCBandUMI.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloReadFeature.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloReadFeature_record.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloReadFeature_inputRecords.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  Solo.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloFeature.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloFeature_collapseUMI.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloFeature_outputResults.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SoloFeature_processRecords.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  ReadAlign_outputAlignments.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  ReadAlign.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  STAR.cpp
In file included from /usr/local/lib/gcc9/include/c++/vector:72,
                 from IncludeDefine.h:14,
                 from STAR.cpp:4:
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void 
std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, 
_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned 
int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:426:7: note: parameter passing 
for argument of type 'std::vector<long long unsigned int>::iterator' {aka 
'__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long 
unsigned int> >'} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc9/include/c++/bits/vector.tcc: In member function 'void 
std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long 
unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long 
unsigned int>]':
/usr/local/lib/gcc9/include/c++/bits/vector.tcc:121:4: note: parameter passing 
for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, 
std::vector<long long unsigned int> >' changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SharedMemory.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  PackedArray.cpp
g++9 -c   -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Wed Sep 
11 05:03:01 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' 
-O2 -pipe  -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9  
-Wl,-rpath=/usr/local/lib/gcc9  SuffixArrayFuns.cpp
In file included from SuffixArrayFuns.h:4,
                 from SuffixArrayFuns.cpp:1:
SuffixArrayFuns.cpp: In function 'long long unsigned int 
funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, 
int&)':
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean 
'__uint32_t'?
   58 | #define uint128 __uint128_t
      |                 ^~~~~~~~~~~
SuffixArrayFuns.cpp:350:18: note: in expansion of macro 'uint128'
  350 |         register uint128 g1=*( (uint128*) (gSeq+SAstr) );
      |                  ^~~~~~~
SuffixArrayFuns.cpp:353:37: error: 'g1' was not declared in this scope; did you 
mean 'g2'?
  353 |             register char g2=(char) g1;
      |                                     ^~
      |                                     g2
In file included from SuffixArrayFuns.h:4,
                 from SuffixArrayFuns.cpp:1:
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean 
'__uint32_t'?
   58 | #define uint128 __uint128_t
      |                 ^~~~~~~~~~~
SuffixArrayFuns.cpp:367:18: note: in expansion of macro 'uint128'
  367 |         register uint128 g1=*( (uint128*) 
(gSeq+mapGen.nGenome-SAstr-16) );
      |                  ^~~~~~~
SuffixArrayFuns.cpp:370:38: error: 'g1' was not declared in this scope; did you 
mean 'g2'?
  370 |             register char g2=(char) (g1>>(8*(15-ii)));
      |                                      ^~
      |                                      g2
SuffixArrayFuns.cpp:341:29: warning: unused parameter 'gSeq' 
[-Wunused-parameter]
  341 | uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Genome &mapGen, 
uint iSA, int L, int & iL4)
      |                       ~~~~~~^~~~
gmake[1]: *** [Makefile:66: SuffixArrayFuns.o] Error 1
gmake[1]: Leaving directory 
'/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source'
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/star
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