ShortRead 1.2.1
Biocore Team c/o BioC user list
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/ShortRead | | Last Changed Rev: 39750 / Revision: 42512 | | Last Changed Date: 2009-05-27 20:44:43 -0700 (Wed, 27 May 2009) |
| wilson1 | 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 |
* checking for file 'ShortRead/DESCRIPTION' ... OK
* preparing 'ShortRead':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o
alphabet.c: In function 'alphabet_as_int':
alphabet.c:195: warning: 'ians' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:125: warning: suggest parentheses around assignment used as truth value
io.c:136: warning: suggest parentheses around assignment used as truth value
io.c:142: warning: suggest parentheses around assignment used as truth value
io.c:117: warning: 'bytes_read' may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c pileup.c -o pileup.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.4-bioc/R/include -I/usr/local/include -I"/home/biocbuild/bbs-2.4-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-2.4-bioc/R/library/Biostrings/include" -fpic -g -O2 -Wall -c util.c -o util.o
util.c: In function '_char_as_strand_int':
util.c:69: warning: 'strand' may be used uninitialized in this function
util.c: In function 'decoder':
util.c:33: warning: 'decode' may be used uninitialized in this function
g++ -shared -L/usr/local/lib64 -o ShortRead.so 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 -lz -L/home/biocbuild/bbs-2.4-bioc/R/lib -lR
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from package:base :
cbind,
duplicated,
order,
pmax,
pmax.int,
pmin,
pmin.int,
rank,
rbind,
rep.int,
sapply,
sort,
table,
unique
Warning in .reportSuperclassConflicts(Class, classDef@contains, where) :
unable to find a consistent ordering of superclasses for class "ArrayIntensity": order chosen is inconsistent with the superclasses of "array"
** help
*** installing help indices
>>> Building/Updating help pages for package 'ShortRead'
Formats: text html latex example
AlignedDataFrame-class text html latex
AlignedDataFrame text html latex
AlignedRead-class text html latex example
AlignedRead text html latex
BowtieQA-class text html latex example
ExperimentPath-class text html latex example
FastqQA-class text html latex example
Intensity-class text html latex example
MAQMapQA-class text html latex example
QA-class text html latex example
QualityScore-class text html latex example
QualityScore text html latex example
RochePath-class text html latex example
RocheSet-class text html latex example
SRFilter-class text html latex example
SRSet-class text html latex example
SRUtil-class text html latex example
ShortRead-class text html latex example
ShortRead-package text html latex
ShortReadQ-class text html latex example
SolexaExportQA-class text html latex example
SolexaIntensity-class text html latex example
SolexaIntensity text html latex
SolexaPath-class text html latex example
SolexaSet-class text html latex example
accessors text html latex example
alphabetByCycle text html latex example
alphabetScore text html latex
clean text html latex example
countLines text html latex example
deprecated text html latex
detail text html latex example
dustyScore text html latex example
pileup text html latex example
polyn text html latex example
qa text html latex example
readAligned text html latex example
readBaseQuality text html latex example
readBfaToc text html latex
readFastq text html latex example
readIntensities text html latex example
readPrb text html latex example
readQseq text html latex example
readXStringColumns text html latex example
report text html latex example
srFilter text html latex example
srapply text html latex example
srdistance text html latex example
srduplicated text html latex example
tables text html latex example
** building package indices ...
* DONE (ShortRead)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'ShortRead_1.2.1.tar.gz'