[package - main-amd64-default][biology/bamutil] Failed for bamutil-1.0.15 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sun, 11 Dec 2022 09:19:35 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/beefy18/data/main-amd64-default/p34cc6c5bcc7c_s08b05de1e2/logs/bamutil-1.0.15.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p34cc6c5bcc7c_s08b05de1e2
Log:

=>> Building biology/bamutil
build started at Sun Dec 11 09:14:37 UTC 2022
port directory: /usr/ports/biology/bamutil
package name: bamutil-1.0.15
building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400074 amd64
maintained by: jwb@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400074
Job Id: 10




!!! Jail is newer than host. (Jail: 1400074, Host: 1400073) !!!
!!! 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-1.18.4.pkg
[main-amd64-default-job-10] Installing pkg-1.18.4...
[main-amd64-default-job-10] Extracting pkg-1.18.4: .......... 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
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
=> SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz.
=> SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by bamutil-1.0.15 for building
===>  Extracting for bamutil-1.0.15
=> SHA256 Checksum OK for statgen-bamUtil-v1.0.15_GH0.tar.gz.
=> SHA256 Checksum OK for statgen-libStatGen-v1.0.15_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for bamutil-1.0.15
===>  Applying FreeBSD patches for bamutil-1.0.15 from /usr/ports/biology/bamutil/files
===========================================================================
=======================<phase: build-depends  >============================
===>   bamutil-1.0.15 depends on package: gmake>=4.3 - not found
===>   Installing existing package /packages/All/gmake-4.3_2.pkg
<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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/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/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/debug/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.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_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o
mkdir -p ../obj/debug
mkdir -p ../bin/debug
gmake -C /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen --no-print-directory profile
mkdir -p obj/profile
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
cc -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/profile/bgzf.o -c bgzf.c 
mkdir -p ../obj/profile
cc -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/profile/knetfile.o -c knetfile.c 
mkdir -p ../bin/profile
ar -cr ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
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="\"Sun Dec 11 09:17:26 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Validate.o -c Validate.cpp -DVERSION="\"1.0.15\""
mkdir -p obj/profile
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/profile/BaseAsciiMap.o -c BaseAsciiMap.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/profile/BaseQualityHelper.o -c BaseQualityHelper.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/profile/BaseUtilities.o -c BaseUtilities.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/profile/BasicHash.o -c BasicHash.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/profile/BgzfFileType.o -c BgzfFileType.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/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:26 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CharBuffer.o -c CharBuffer.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/profile/Chromosome.o -c Chromosome.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/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:32 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CigarRoller.o -c CigarRoller.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/profile/Error.o -c Error.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/profile/ErrorHandler.o -c ErrorHandler.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/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:38 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FortranFormat.o -c FortranFormat.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/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:44 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:48 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/glfHandler.o -c glfHandler.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/profile/GzipFileType.o -c GzipFileType.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/profile/GzipHeader.o -c GzipHeader.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/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:53 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IndexBase.o -c IndexBase.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/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:17:57 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/InputFile.o -c InputFile.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/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:00 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IntHash.o -c IntHash.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/profile/LongLongCounter.o -c LongLongCounter.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/profile/MapFunction.o -c MapFunction.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/profile/MathMatrix.o -c MathMatrix.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/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:02 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryAllocators.o -c MemoryAllocators.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/profile/MemoryInfo.o -c MemoryInfo.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/profile/MemoryMapArray.o -c MemoryMapArray.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/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:07 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MiniDeflate.o -c MiniDeflate.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/profile/NonOverlapRegions.o -c NonOverlapRegions.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/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:11 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.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/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:14 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeDescription.o -c PedigreeDescription.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/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:18 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.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/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:22 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PhoneHome.o -c PhoneHome.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/profile/QuickIndex.o -c QuickIndex.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/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:26 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/ReferenceSequence.o -c ReferenceSequence.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/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:30 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/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/profile/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/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:33 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/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/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:36 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/SplitBam.o -c SplitBam.cpp -DVERSION="\"1.0.15\""
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/profile/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/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:39 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/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/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:42 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/MergeBam.o -c MergeBam.cpp -DVERSION="\"1.0.15\""
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/profile/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/profile/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/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
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="\"Sun Dec 11 09:18:44 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj
 /profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
mkdir -p obj/profile
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/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
mkdir -p obj/profile
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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o
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="\"Sun Dec 11 09:18:48 UTC 2022\"" -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../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/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/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
mkdir -p obj/profile
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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o
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/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
mkdir -p obj/profile
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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/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/profile/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.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/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cr ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o
ar -cr ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o
ar: fatal: Incorrect file header signature: Invalid argument
gmake[4]: *** [../Makefiles/Makefile.lib:41: ../libStatGen_profile.a] Error 1
gmake[3]: *** [Makefiles/Makefile.base:15: bam] Error 2
gmake[3]: *** Waiting for unfinished jobs....
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="\"Sun Dec 11 09:18:56 UTC 2022\"" -DVERSION="\"1.0.15\"" -DUSER="\"root\"" -o ../obj/Logger.o -c Logger.cpp -DVERSION="\"1.0.15\""
gmake[2]: *** [/wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/Makefiles/Makefile.ext:54: /wrkdirs/usr/ports/biology/bamutil/work/bamUtil-1.0.15/libStatGen/libStatGen_profile.a] Error 2
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'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1

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