Bioconductor Package Maintainer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rsamtools |
| Branch: RELEASE_3_8 |
| Last Commit: 0ec1d45 |
| Last Changed Date: 2019-01-30 18:10:29 -0400 (Wed, 30 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:53 -0400 (Tue, 16 Apr 2019).
| Package 1352/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rsamtools 1.34.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | [ OK ] | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: Rsamtools |
| Version: 1.34.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Rsamtools |
| StartedAt: 2019-04-15 18:11:04 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 18:11:44 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 39.6 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Rsamtools
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c ResultManager.cpp -o ResultManager.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 idxstats.c -o idxstats.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c pileup.cpp -o pileup.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I/usr/local/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
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/bcftools"
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/tabix"
cp samtools/*.h "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include/tabix/"
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib"
g++ -shared -L/home/biocbuild/bbs-3.8-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 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 /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/libbam.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/libbcf.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)