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INSTALL report for Rsamtools on tokay2

This page was generated on 2018-10-17 08:34:41 -0400 (Wed, 17 Oct 2018).

Package 1281/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 1.32.3
Bioconductor Package Maintainer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Rsamtools
Branch: RELEASE_3_7
Last Commit: 0aa3f13
Last Changed Date: 2018-08-22 05:19:22 -0400 (Wed, 22 Aug 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsamtools
Version: 1.32.3
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rsamtools_1.32.3.tar.gz && rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_1.32.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rsamtools_1.32.3.zip && rm Rsamtools_1.32.3.tar.gz Rsamtools_1.32.3.zip
StartedAt: 2018-10-16 19:29:55 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:34:05 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 250.4 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rsamtools_1.32.3.tar.gz && rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_1.32.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rsamtools_1.32.3.zip && rm Rsamtools_1.32.3.tar.gz Rsamtools_1.32.3.zip
###
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100 2695k  100 2695k    0     0  25.6M      0 --:--:-- --:--:-- --:--:-- 27.4M

install for i386

* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c as_bam.c -o as_bam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bam_data.c -o bam_data.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from BamRangeIterator.h:7:0,
                 from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bamfile.c -o bamfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bcffile.c -o bcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c encode.c -o encode.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c fafile.c -o fafile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c idxstats.c -o idxstats.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c io_sam.c -o io_sam.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pileup.cpp -o pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'worker_aux':
samtools/bgzf.c:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:169:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
                 abort();
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
  bam_header_t *old;
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_32/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_32/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_32/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools\mingw_32\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rsamtools'
    finding HTML links ... done
    ApplyPileupsParam-class                 html  
    BamFile-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/BamFile-class.Rd:350: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/BamFile-class.Rd:351: file link 'readGAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/BamFile-class.Rd:354: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    BamViews-class                          html  
    BcfFile-class                           html  
    FaFile-class                            html  
    PileupFiles-class                       html  
    Rsamtools-package                       html  
    RsamtoolsFile-class                     html  
    RsamtoolsFileList-class                 html  
    ScanBamParam-class                      html  
    ScanBcfParam-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:62: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:65: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:69: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:138: file link 'scanVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:139: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
    TabixFile-class                         html  
    applyPileups                            html  
    defunct                                 html  
    deprecated                              html  
    headerTabix                             html  
    indexTabix                              html  
    pileup                                  html  
    quickBamFlagSummary                     html  
    readPileup                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    scanBam                                 html  
    scanBcf                                 html  
    scanFa                                  html  
    scanTabix                               html  
    seqnamesTabix                           html  
    testPairedEndBam                        html  
    zip                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c as_bam.c -o as_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bam_data.c -o bam_data.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from BamRangeIterator.h:7:0,
                 from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bamfile.c -o bamfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bcffile.c -o bcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c encode.c -o encode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c fafile.c -o fafile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c idxstats.c -o idxstats.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c io_sam.c -o io_sam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pileup.cpp -o pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'worker_aux':
samtools/bgzf.c:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:169:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
                 abort();
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
  bam_header_t *old;
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_64/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_64/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_64/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools\mingw_64\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.32.3.zip
* DONE (Rsamtools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Rsamtools' successfully unpacked and MD5 sums checked
In R CMD INSTALL