ShortRead 1.4.0
Biocore Team c/o BioC user list
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/ShortRead | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | [ OK ] |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'ShortRead' ...
** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c alphabet.c -o alphabet.o
alphabet.c: In function 'alphabet_as_int':
alphabet.c:190: warning: 'ians' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:118: warning: 'bytes_read' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_bowtie.c -o io_bowtie.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c io_soap.c -o io_soap.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c pileup.c -o pileup.o
g++ -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c util.c -o util.o
util.c: In function '_char_as_strand_int':
util.c:95: warning: 'strand' may be used uninitialized in this function
util.c: In function 'encoder':
util.c:59: warning: 'encode' may be used uninitialized in this function
util.c: In function 'decoder':
util.c:43: warning: 'decode' may be used uninitialized in this function
gcc -I"E:/biocbld/bbs-2.5-bioc/R/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.5-bioc/R/library/Biostrings/include" -O3 -Wall -std=gnu99 -c xsnap.c -o xsnap.o
g++ -shared -s -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o util.o xsnap.o -lRzlib -LE:/biocbld/bbs-2.5-bioc/R/bin -lR
... done
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
Map,
cbind,
mapply,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rbind,
rep.int,
table
** help
*** installing help indices
** building package indices ...
** MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.4.0.zip
* DONE (ShortRead)