Rsamtools 1.3.23
Biocore Team c/o BioC user list
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools | | Last Changed Rev: 53004 / Revision: 53255 | | Last Changed Date: 2011-02-19 14:37:54 -0800 (Sat, 19 Feb 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | [ OK ] |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | WARNINGS | OK |
* installing *source* package 'Rsamtools' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c fafile.c -o fafile.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bamfile.c -o bamfile.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c io_sam.c -o io_sam.o
In file included from E:/biocbld/bbs-2.8-bioc/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from io_sam.c:3:
E:/biocbld/bbs-2.8-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c as_bam.c -o as_bam.o
In file included from E:/biocbld/bbs-2.8-bioc/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from as_bam.c:2:
E:/biocbld/bbs-2.8-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c utilities.c -o utilities.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c encode.c -o encode.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcffile.c -o bcffile.o
In file included from E:/biocbld/bbs-2.8-bioc/R/include/Rdefines.h:26:0,
from bcffile.h:4,
from bcffile.c:5:
E:/biocbld/bbs-2.8-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools212\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam.c -o samtools/bam.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam_import.c -o samtools/bam_import.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c:294:1: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
samtools/bam_sort.c:53:1: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: too many arguments for format
samtools/bam_index.c:528:2: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:528:2: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/kstring.c -o samtools/kstring.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/razf.c -o samtools/razf.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:414:5: warning: unknown conversion type character 'l' in format
samtools/knetfile.c:414:5: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/sam.c -o samtools/sam.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c samtools/faidx.c -o samtools/faidx.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/bcf.c -o bcftools/bcf.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/vcf.c -o bcftools/vcf.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/bcfutils.c -o bcftools/bcfutils.o
bcftools/bcfutils.c: In function 'bcf_shrink_alt':
bcftools/bcfutils.c:64:2: warning: implicit declaration of function 'alloca'
bcftools/bcfutils.c:64:6: warning: incompatible implicit declaration of built-in function 'alloca'
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/prob1.c -o bcftools/prob1.o
bcftools/prob1.c: In function 'cal_pdg':
bcftools/prob1.c:189:2: warning: implicit declaration of function 'alloca'
bcftools/prob1.c:189:6: warning: incompatible implicit declaration of built-in function 'alloca'
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/ld.c -o bcftools/ld.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/kfunc.c -o bcftools/kfunc.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/index.c -o bcftools/index.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/fet.c -o bcftools/fet.o
gcc -I"E:/biocbld/bbs-2.8-bioc/R/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.8-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -O3 -Wall -std=gnu99 -c bcftools/bcf2qcall.c -o bcftools/bcf2qcall.o
gcc -shared -s -static-libgcc -o Rsamtools.dll tmp.def fafile.o bamfile.o io_sam.o as_bam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o bcffile.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_sort.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o bcftools/bcf.o bcftools/vcf.o bcftools/bcfutils.o bcftools/prob1.o bcftools/ld.o bcftools/kfunc.o bcftools/index.o bcftools/fet.o bcftools/bcf2qcall.o -lRzlib -lws2_32 -LE:/biocbld/bbs-2.8-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported? Making a copy in package 'Rsamtools'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.3.23.zip
* DONE (Rsamtools)