Package: GeneRegionScan

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.13.1.tar.gz

StartedAt: 2012-06-21 00:13:30 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:20:46 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 436.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GeneRegionScan.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.13.1'
* 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 whether package 'GeneRegionScan' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    exec  19.7Mb
* 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 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
readGeneInput: warning in readFASTA(gene, strip.desc = FALSE): partial
  argument match of 'strip.desc' to 'strip.descs'
* 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 sizes of PDF files under 'inst/doc' ... 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
  '/Users/biocbuild/bbs-2.11-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.

* installing *source* package 'GeneRegionScan' ...
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneRegionScan.Rnw' 
** testing if installed package can be loaded

* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0.001	0.000	0.001
checkForFileInPath	0.017	0.007	0.112
doProbeLinear	3.460	0.037	3.641
doProbeTTest	0.643	0.006	0.672
exampleProbeLevelSet	0.034	0.016	0.050
excludeDoubleMatchingProbes	0	0	0
exonStructure	13.744	0.095	14.664
findProbePositions	0.578	0.008	0.592
findSequenceInGenome	0	0	0
geneRegionScan	101.493	29.657	138.286
getLocalMetaprobeIntensities	0.000	0.000	0.001
getLocalProbeIntensities	0.001	0.000	0.000
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0.000	0.001	0.001
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0	0	0
getSequence	0.023	0.010	0.033
getServerProbeIntensities	0.000	0.000	0.001
plotCoexpression	75.857	27.343	104.601
plotOnGene	22.486	0.092	22.835
readGeneInput	0.001	0.000	0.000
translateSampleNames	0.089	0.007	0.096