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BioC 3.1: INSTALL report for Rsamtools on zin2

This page was generated on 2015-10-09 09:23:59 -0700 (Fri, 09 Oct 2015).

Package 852/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 1.20.5
Bioconductor Package Maintainer
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/Rsamtools
Last Changed Rev: 109036 / Revision: 109384
Last Changed Date: 2015-09-30 17:42:34 -0700 (Wed, 30 Sep 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsamtools
Version: 1.20.5
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL Rsamtools
StartedAt: 2015-10-08 18:03:22 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:03:59 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 36.6 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.1-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c bam_data.c -o bam_data.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -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:81:10: 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:84:5: 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:84:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c encode.c -o encode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c fafile.c -o fafile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c io_sam.c -o io_sam.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/include"   -fpic  -g -O2  -Wall -c pileup.cpp -o pileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -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;
           ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_index.c -o samtools/bam_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/razf.c -o samtools/razf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/knetfile.c -o samtools/knetfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -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;
                ^
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -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;
                     ^
ar -crus 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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus 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
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.1-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.1-bioc/R/library/Biostrings/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 -fpic  -g -O2  -Wall -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/bcftools"
mkdir -p "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/tabix"
cp samtools/*.h "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
		"/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/include/tabix/"
mkdir -p "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib"
g++ -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o Rsamtools.so 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 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 /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib/libbam.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib/libbcf.a /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/R/library/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rsamtools-Overview.Rnw’ 
   ‘Rsamtools-UsingCLibraries.Rnw’ 
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Rsamtools)