[package - main-armv6-default][biology/bamutil] Failed for bamutil-1.0.15 in build
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Date: Thu, 27 Jul 2023 06:13:52 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/p5cfda4f9e5a4_s474708c334/logs/bamutil-1.0.15.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p5cfda4f9e5a4_s474708c334
Log:
=>> Building biology/bamutil
build started at Thu Jul 27 04:57:25 UTC 2023
port directory: /usr/ports/biology/bamutil
package name: bamutil-1.0.15
building for: FreeBSD main-armv6-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1400088
Jail OSVERSION: 1400093
Job Id: 07
!!! Jail is newer than host. (Jail: 1400093, Host: 1400088) !!!
!!! 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 >============================
===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-armv6-default-job-07] Installing pkg-1.20.4...
[main-armv6-default-job-07] Extracting pkg-1.20.4: .......... done
===> bamutil-1.0.15 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bamutil-1.0.15
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
<snip>
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
In file included from ReferenceSequence.cpp:25:
./ReferenceSequence.h:315:39: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while((ch = inputStream.ifgetc()) != EOF) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~
./ReferenceSequence.h:327:68: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while (!isspace((ch = inputStream.ifgetc())) && ch != EOF)
~~ ^ ~~~
./ReferenceSequence.h:336:28: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
} while(ch != EOF && ch != '\n' && ch != '\r');
~~ ^ ~~~
3 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.
o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h
ln -s ../bam/SamFile.h ../include/SamFile.h
ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h
ln -s ../bam/SamInterface.h ../include/SamInterface.h
ln -s ../bam/BamInterface.h ../include/BamInterface.h
ln -s ../bam/SamRecord.h ../include/SamRecord.h
ln -s ../bam/BamIndex.h ../include/BamIndex.h
ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h
ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h
ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h
ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h
ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h
ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h
ln -s ../bam/SamValidation.h ../include/SamValidation.h
ln -s ../bam/SamStatistics.h ../include/SamStatistics.h
ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h
ln -s ../bam/SamFilter.h ../include/SamFilter.h
ln -s ../bam/PileupElement.h ../include/PileupElement.h
ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h
ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h
ln -s ../bam/SamTags.h ../include/SamTags.h
ln -s ../bam/PosList.h ../include/PosList.h
ln -s ../bam/CigarHelper.h ../include/CigarHelper.h
ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h
ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h
ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h
ln -s ../bam/Pileup.h ../include/Pileup.h
ln -s ../bam/SamHelper.h ../include/SamHelper.h
ln -s ../bam/SamFlag.h ../include/SamFlag.h
ln -s ../bam/SamStatus.h ../include/SamStatus.h
mkdir -p obj
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
ln -s ../fastq/FastQFile.h ../include/FastQFile.h
ln -s ../fastq/BaseCount.h ../include/BaseCount.h
ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h
ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h
mkdir -p obj
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
ln -s ../glf/GlfException.h ../include/GlfException.h
ln -s ../glf/GlfFile.h ../include/GlfFile.h
ln -s ../glf/GlfHeader.h ../include/GlfHeader.h
ln -s ../glf/GlfRecord.h ../include/GlfRecord.h
ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h
ln -s ../glf/GlfStatus.h ../include/GlfStatus.h
mkdir -p obj
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
ln -s ../vcf/VcfFile.h ../include/VcfFile.h
ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h
ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h
ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h
ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h
ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h
ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h
ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h
ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h
ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h
ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h
ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h
ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h
ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h
ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h
mkdir -p obj
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o
mkdir -p ../obj
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:49:56 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:50:39 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Convert.o -c Convert.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:51:14 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Diff.o -c Diff.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:52:08 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpHeader.o -c DumpHeader.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:52:39 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitChromosome.o -c SplitChromosome.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:53:10 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/WriteRegion.o -c WriteRegion.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:53:50 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpIndex.o -c DumpIndex.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:54:20 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ReadIndexedBam.o -c ReadIndexedBam.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:54:51 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/DumpRefInfo.o -c DumpRefInfo.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:55:23 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Filter.o -c Filter.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:55:59 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ReadReference.o -c ReadReference.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:56:31 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Revert.o -c Revert.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:57:04 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Squeeze.o -c Squeeze.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:57:44 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/FindCigars.o -c FindCigars.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:58:16 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Stats.o -c Stats.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:58:59 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/PileupElementBaseQCStats.o -c PileupElementBaseQCStats.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 05:59:30 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ClipOverlap.o -c ClipOverlap.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:00:07 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MateMapByCoord.o -c MateMapByCoord.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:00:40 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\""
SplitBam.cpp:119:101: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while ( ( c = getopt_long(argc-1, &(argv[1]), "i:o:vLn:", getopt_long_options, &n_option_index) ) != -1 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:01:18 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/TrimBam.o -c TrimBam.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:01:53 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\""
MergeBam.cpp:150:99: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while ( ( c = getopt_long(argc, argv, "l:i:o:vIL:r:R:", getopt_long_options, &n_option_index) ) != -1 ) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~
1 warning generated.
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:02:50 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/PolishBam.o -c PolishBam.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:03:49 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/GapInfo.o -c GapInfo.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:04:31 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:04:58 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Bam2FastQ.o -c Bam2FastQ.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:05:49 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Dedup.o -c Dedup.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:06:55 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Dedup_LowMem.o -c Dedup_LowMem.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:08:00 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Prediction.o -c Prediction.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:08:31 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/LogisticRegression.o -c LogisticRegression.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:09:00 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MathCholesky.o -c MathCholesky.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:09:26 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/HashErrorModel.o -c HashErrorModel.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:10:06 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Recab.o -c Recab.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:10:58 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/OverlapHandler.o -c OverlapHandler.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:11:31 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/OverlapClipLowerBaseQual.o -c OverlapClipLowerBaseQual.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:12:03 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/ExplainFlags.o -c ExplainFlags.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:12:36 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Main.o -c Main.cpp -DVERSION="\"1.0.15\""
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:13:23 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/BamExecutable.o -c BamExecutable.cpp -DVERSION="\"1.0.15\""
mkdir -p ../bin
c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thu Jul 27 06:13:49 UTC 2023\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../bin/bam ../obj/BamExecutable.o ../obj/Validate.o ../obj/Convert.o ../obj/Diff.o ../obj/DumpHeader.o ../obj/SplitChromosome.o ../obj/WriteRegion.o ../obj/DumpIndex.o ../obj/ReadIndexedBam.o ../obj/DumpRefInfo.o ../obj/Filter.o ../obj/ReadReference.o ../obj/Revert.o ../obj/Squeeze.o ../obj/FindCigars.o ../obj/Stats.o ../obj/PileupElementBaseQCStats.o ../obj/ClipOverlap.o ../obj/MateMapByCoord.o ../obj/SplitBam.o ../obj/TrimBam.o ../obj/MergeBam.o ../obj/PolishBam.o ../obj/GapInfo.o ../obj/Logger.o ../obj/Bam2FastQ.o ../obj/Dedup.o ../obj/Dedup_LowMem.o ../obj/Prediction.o ../obj/LogisticRegression.o ../obj/MathCholesky.o ../obj/HashErrorModel.o ../obj/Recab.o ../obj/OverlapHan
dler.o ../obj/OverlapClipLowerBaseQual.o ../obj/ExplainFlags.o ../obj/Main.o /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen.a -lm -lz
c++: error: unable to execute command: Abort trap (core dumped)
c++: error: linker command failed due to signal (use -v to see invocation)
gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:40: ../bin/bam] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/src'
gmake[1]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.base:15: src] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bamutil