Package: GeneRegionScan

Version: 1.15.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.15.5.tar.gz

StartedAt: 2013-03-24 05:33:34 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:40:32 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 417.8 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.15.5'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GeneRegionScan' can be installed ... [14s/16s] 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 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
plotOnGene,ExpressionSet: warning in plot.default(1, type = "n", xlab =
  "bp", ylab = ylab, frame = FALSE, xlim = xlim, ylim = ylim, main =
  paste("Expression of probes"), cex.main = 1): partial argument match
  of 'frame' to 'frame.plot'
plotCoexpression,ExpressionSet: no visible binding for global variable
  'interval'
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [256s/263s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   95.717 20.246 120.423
plotCoexpression 70.839 21.664  93.830
plotOnGene       22.106  0.138  22.372
exonStructure    13.215  0.139  13.989
* 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-2.12-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	0.223	0.003	0.226
checkForFileInPath	0.027	0.010	0.178
doProbeLinear	3.119	0.060	3.313
doProbeTTest	0.679	0.016	0.695
exampleProbeLevelSet	0.048	0.017	0.065
excludeDoubleMatchingProbes	0.244	0.004	0.249
exonStructure	13.215	0.139	13.989
findProbePositions	0.822	0.021	0.860
findSequenceInGenome	0.007	0.005	0.012
geneRegionScan	95.717	20.246	120.423
getLocalMetaprobeIntensities	0.004	0.006	0.011
getLocalProbeIntensities	0.004	0.006	0.010
getMetaprobesetsFromRegionOfInterest	0.003	0.006	0.009
getProbeLevelAnnotationForExonArrays	0.003	0.007	0.010
getProbesetsFromMetaprobeset	0.003	0.008	0.011
getProbesetsFromRegionOfInterest	0.003	0.007	0.009
getSequence	0.024	0.016	0.039
getServerProbeIntensities	0.004	0.009	0.014
plotCoexpression	70.839	21.664	93.830
plotOnGene	22.106	0.138	22.372
readGeneInput	0.003	0.006	0.010
translateSampleNames	0.089	0.015	0.105