Rsamtools 1.16.1
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rsamtools | | Last Changed Rev: 91340 / Revision: 95116 | | Last Changed Date: 2014-06-12 15:06:53 -0700 (Thu, 12 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rsamtools_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-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 ‘1.16.1’
* 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 ... [26s/27s] OK
* checking installed package size ... NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
extdata 2.6Mb
libs 2.0Mb
usrlib 1.7Mb
* 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:
‘BiocGenerics:::selectSome’ ‘IRanges:::explodeIntBits’
‘IRanges:::implodeIntBits’ ‘IRanges:::makePowersOfTwo’
See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/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.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘Rsamtools_unit_tests.R’ [31s/38s]
[31s/39s] 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
NOTE: There were 3 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c as_bam.c -o as_bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c bambuffer.c -o bambuffer.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c bamfile.c -o bamfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c bcffile.c -o bcffile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c encode.c -o encode.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c fafile.c -o fafile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c pileupbam.c -o pileupbam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools_patch.c -o samtools_patch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c scan_bam_data.c -o scan_bam_data.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c tabixfile.c -o tabixfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c utilities.c -o utilities.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c zip_compression.c -o zip_compression.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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]
samtools/bgzf.c: In function ‘bgzf_close’:
samtools/bgzf.c:592:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/kstring.c -o samtools/kstring.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam.c -o samtools/bam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_import.c -o samtools/bam_import.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/sam.c -o samtools/sam.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_index.c -o samtools/bam_index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_md.c -o samtools/bam_md.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/razf.c -o samtools/razf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/faidx.c -o samtools/faidx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/knetfile.c -o samtools/knetfile.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/sam_header.c -o samtools/sam_header.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -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]
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-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c tabix/index.c -o tabix/index.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-2.14-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-2.14-bioc/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
cp ../Rsamtools.mk "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
mkdir -p "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools"
mkdir -p "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix"
cp samtools/*.h "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
mkdir -p "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
g++ -shared -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.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 pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp /home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbam.a /home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbcf.a /home/biocbuild/bbs-2.14-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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)