Rsamtools 1.8.6
Bioconductor Package Maintainer
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/Rsamtools | | Last Changed Rev: 68208 / Revision: 69725 | | Last Changed Date: 2012-08-04 15:50:49 -0700 (Sat, 04 Aug 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ WARNINGS ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.8.6’
* 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 whether package ‘Rsamtools’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
extdata 1.7Mb
libs 1.3Mb
usrlib 1.8Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* 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 ... WARNING
Undocumented code objects:
‘showGappedAlignmentsEltsWithMoreThan1Mate’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs/Rsamtools.so’:
Found ‘stderr’, possibly from ‘stderr’ (C)
Object: ‘samtools_patch.o’
Compiled code should not call functions 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 examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.
* installing *source* package ‘Rsamtools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bam_import.c: In function ‘__bam_get_lines’:
samtools/bam_import.c:76:2: warning: implicit declaration of function ‘gzopen64’
samtools/bam_import.c:76:66: warning: pointer/integer type mismatch in conditional expression
samtools/bam_import.c: In function ‘sam_header_read2’:
samtools/bam_import.c:126:59: warning: pointer/integer type mismatch in conditional expression
samtools/bam_import.c: In function ‘sam_open’:
samtools/bam_import.c:472:69: warning: pointer/integer type mismatch in conditional expression
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bcftools/vcf.c: In function ‘vcfFile_open’:
samtools/bcftools/vcf.c:27:3: warning: implicit declaration of function ‘gzopen64’
samtools/bcftools/vcf.c:27:14: warning: assignment makes pointer from integer without a cast
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bcftools/prob1.c: In function ‘bcf_p1_read_prior’:
samtools/bcftools/prob1.c:96:2: warning: implicit declaration of function ‘gzopen64’
samtools/bcftools/prob1.c:96:40: warning: pointer/integer type mismatch in conditional expression
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -Wall -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.10-bioc/R/include -DNDEBUG -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Biostrings/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/IRanges/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
tabix/bedidx.c: In function ‘bed_read’:
tabix/bedidx.c:103:2: warning: implicit declaration of function ‘gzopen64’
tabix/bedidx.c:103:40: warning: pointer/integer type mismatch in conditional expression
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
cp ../Rsamtools.mk "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc"
mkdir -p "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools"
mkdir -p "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix"
cp samtools/*.h "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/"
mkdir -p "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib"
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o zip_compression.o -fopenmp /loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbam.a /loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libbcf.a /loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/libtabix.a -lz -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘Rsamtools-Overview.Rnw’
‘Rsamtools-UsingCLibraries.Rnw’
** testing if installed package can be loaded
* DONE (Rsamtools)