Package: rnaSeqMap

Version: 2.13.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings rnaSeqMap_2.13.1.tar.gz

StartedAt: 2013-01-16 06:00:55 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:04:58 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 243.1 seconds

RetCode: 0

Status:  OK

CheckDir: rnaSeqMap.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaSeqMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnaSeqMap’ version ‘2.13.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rnaSeqMap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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
qq_derivative_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F):
  partial argument match of 'plot' to 'plot.it'
qq_plot: warning in qqplot(dd[, 1], dd[, 2], , plot = F): partial
  argument match of 'plot' to 'plot.it'
bam2sig: no visible global function definition for ‘dbGetQuery’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/00check.log’
for details.

* installing *source* package ‘rnaSeqMap’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gcoverage.c -o gcoverage.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ghistogram.c -o ghistogram.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c regionmining.c -o regionmining.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c splicingind.c -o splicingind.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘rnaSeqMap.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (rnaSeqMap)

name	user	system	elapsed
NDplots	0.108	0.004	0.112
RleList2matrix	0.012	0.000	0.011
addBamData	0.008	0.000	0.007
addDataToReadset	0.112	0.000	0.111
addExperimentsToReadset	0.012	0.000	0.010
averageND	0.012	0.000	0.012
bam2sig	0.012	0.000	0.011
buildDESeq	0.012	0.000	0.011
buildDGEList	0.012	0.000	0.011
findRegionsAsIR	0.008	0.000	0.008
findRegionsAsND	0.008	0.000	0.007
gRanges2CamelMeasures	0.008	0.000	0.006
geneInChromosome	0.012	0.000	0.010
generators	0.012	0.000	0.011
getBamData	0.004	0.000	0.007
getCoverageFromRS	0.016	0.000	0.013
getFCFromND	0.012	0.000	0.013
getSIFromND	0.008	0.000	0.007
getSumsExp	0.012	0.000	0.012
measures	0.008	0.000	0.008
normalizations	0.012	0.000	0.014
normalizeBySum	0.012	0.000	0.014
parseGff3	0.004	0.004	0.008
plotGeneCoverage	0.012	0.000	0.013
readsInRange	0.008	0.000	0.009
regionBasedCoverage	0.012	0.000	0.010
regionCoverage	0.020	0.000	0.017
rs.list	0.064	0.008	0.075
setSpecies	0.008	0.000	0.008
spaceInChromosome	0.016	0.000	0.012