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 working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.4-bioc/meat/ShortRead.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ShortRead/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ShortRead' version '1.2.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ShortRead' can be installed ... OK
* 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 name space can be loaded with stated dependencies ... 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 ... NOTE
.plotCycleBaseCall: no visible binding for global variable 'Base'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ... OK
* checking examples ... OK
* checking tests ...
Running 'runalltests.R'
Comparing 'runalltests.Rout' to 'runalltests.Rout.save' ...19,21c19
< Error in checkEquals(srorder(quality(rfq)), order(as.character(quality(quality(rfq))))) :
< Mean relative difference: 0.6327729
< Error in checkTrue(FALSE) : Test not TRUE
---
> Error in checkTrue(FALSE) : Test not TRUE.
OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* 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)