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: 2013-03-25 02:39:35 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:45:39 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 363.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.15.5'
* 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 ... [12s/12s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [229s/231s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   83.867 21.826 106.255
plotCoexpression 59.202 21.939  81.536
plotOnGene       17.044  0.068  18.240
exonStructure    15.333  0.089  15.439
* 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	0.004	0.005	0.010
checkForFileInPath	0.017	0.011	0.110
doProbeLinear	2.509	0.024	2.534
doProbeTTest	0.802	0.023	0.827
exampleProbeLevelSet	0.059	0.023	0.083
excludeDoubleMatchingProbes	0.015	0.009	0.024
exonStructure	15.333	0.089	15.439
findProbePositions	0.601	0.018	0.620
findSequenceInGenome	0.004	0.007	0.010
geneRegionScan	83.867	21.826	106.255
getLocalMetaprobeIntensities	0.004	0.005	0.009
getLocalProbeIntensities	0.003	0.006	0.009
getMetaprobesetsFromRegionOfInterest	0.003	0.008	0.011
getProbeLevelAnnotationForExonArrays	0.002	0.006	0.008
getProbesetsFromMetaprobeset	0.002	0.006	0.008
getProbesetsFromRegionOfInterest	0.003	0.005	0.008
getSequence	0.024	0.014	0.037
getServerProbeIntensities	0.004	0.009	0.013
plotCoexpression	59.202	21.939	81.536
plotOnGene	17.044	0.068	18.240
readGeneInput	0.004	0.005	0.009
translateSampleNames	0.077	0.015	0.091