Rsamtools 1.28.0
Bioconductor Package Maintainer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/Rsamtools | | Branch: RELEASE_3_5 | | Last Commit: dfa5b6a | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rsamtools_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsamtools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
extdata 2.6Mb
libs 3.0Mb
usrlib 1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘S4Vectors:::explodeIntBits’ ‘S4Vectors:::implodeIntBits’
‘S4Vectors:::makePowersOfTwo’ ‘S4Vectors:::quick_unlist’
‘S4Vectors:::selectSome’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rsamtools/libs/Rsamtools.so’:
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘samtools_patch.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileup 28.52 0.032 28.582
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rsamtools_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c ResultManager.cpp -o ResultManager.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I/usr/local/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:80:10: warning: ‘BamIterator::iter_done’ will be initialized after [-Wreorder]
bool iter_done;
^
BamIterator.h:29:13: warning: ‘bam1_t* BamIterator::bam’ [-Wreorder]
bam1_t *bam;
^
BamIterator.h:83:5: warning: when initialized here [-Wreorder]
BamIterator(bamFile bfile, const bam_index_t *bindex) :
^
BamIterator.h:29:13: warning: ‘BamIterator::bam’ will be initialized after [-Wreorder]
bam1_t *bam;
^
BamIterator.h:15:14: warning: ‘_BAM_DATA* BamIterator::bam_data’ [-Wreorder]
BAM_DATA bam_data;
^
BamIterator.h:83:5: warning: when initialized here [-Wreorder]
BamIterator(bamFile bfile, const bam_index_t *bindex) :
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I/usr/local/include -fpic -g -O2 -Wall -c pileup.cpp -o pileup.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-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-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools"
mkdir -p "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix"
cp samtools/*.h "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
mkdir -p "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
g++ -shared -L/home/biocbuild/bbs-3.5-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-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbam.a /home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbcf.a /home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)