Rsamtools 1.2.3
Biocore Team c/o BioC user list
| Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Rsamtools | | Last Changed Rev: 51873 / Revision: 54588 | | Last Changed Date: 2011-01-11 16:14:33 -0800 (Tue, 11 Jan 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | [ OK ] |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
* installing *source* package 'Rsamtools' ...
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WARNING: this package has a configure script
It probably needs manual configuration
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** libs
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c io_sam.c -o io_sam.o
In file included from E:/biocbld/bbs-2.7-bioc/R/include/Rdefines.h:26:0,
from E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include/IRanges_defines.h:18,
from E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include/IRanges_interface.h:12,
from io_sam.c:5:
E:/biocbld/bbs-2.7-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-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c utilities.c -o utilities.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c encode.c -o encode.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam.c -o samtools/bam.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:166:2: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:166:2: warning: format '%s' expects type 'char *', but argument 3 has type 'int64_t'
samtools/bam_import.c:166:2: warning: too many arguments for format
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:179:13: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
samtools/bam_import.c: In function 'sam_read1':
samtools/bam_import.c:318:5: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:318:5: warning: too many arguments for format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: too many arguments for format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: too many arguments for format
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c:273:1: 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-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_core':
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: too many arguments for format
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-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/kstring.c -o samtools/kstring.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bgzf.c -o samtools/bgzf.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/razf.c -o samtools/razf.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/sam.c -o samtools/sam.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -I"E:/biocbld/bbs-2.7-bioc/R/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.7-bioc/R/library/IRanges/include" -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -O3 -Wall -std=gnu99 -c samtools/faidx.c -o samtools/faidx.o
gcc -shared -s -static-libgcc -o Rsamtools.dll tmp.def io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.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 -lRzlib -lws2_32 -LE:/biocbld/bbs-2.7-bioc/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-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, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.2.3.zip
* DONE (Rsamtools)