Rsamtools 1.23.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD INSTALL Rsamtools
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* installing to library ‘/home/biocbuild/bbs-3.3-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c IRanges_stubs.c -o IRanges_stubs.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c PileupBuffer.cpp -o PileupBuffer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c PosCacheColl.cpp -o PosCacheColl.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c ResultManager.cpp -o ResultManager.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c bam_data.c -o bam_data.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c encode.c -o encode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c fafile.c -o fafile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c io_sam.c -o io_sam.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/Biostrings/include" -fpic -g -O2 -c pileup.cpp -o pileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c tagfilter.c -o tagfilter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_index.c -o samtools/bam_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/razf.c -o samtools/razf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/knetfile.c -o samtools/knetfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bam_reheader.c -o samtools/bam_reheader.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/kprobaln.c -o samtools/kprobaln.o
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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -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-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.3-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 -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-3.3-bioc/R/library/Rsamtools/include/samtools/bcftools"
mkdir -p "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include/tabix"
cp samtools/*.h "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/include/tabix/"
mkdir -p "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib"
g++ -shared -L/home/biocbuild/bbs-3.3-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-3.3-bioc/R/library/Rsamtools/usrlib/libbam.a /home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib/libbcf.a /home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/R/library/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘Rsamtools-Overview.Rnw’
‘Rsamtools-UsingCLibraries.Rnw’
** testing if installed package can be loaded
* DONE (Rsamtools)