Package: GeneRegionScan

Version: 1.15.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GeneRegionScan_1.15.5.tar.gz

StartedAt: 2013-01-16 02:49:26 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:54:43 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 316.9 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.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 ‘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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   73.472 14.904  88.406
plotCoexpression 51.780 15.381  67.162
plotOnGene       18.549  0.004  18.554
exonStructure    11.313  0.032  11.350
* 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/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	0.008	0.000	0.007
checkForFileInPath	0.028	0.004	0.127
doProbeLinear	2.376	0.020	2.397
doProbeTTest	0.564	0.012	0.579
exampleProbeLevelSet	0.268	0.012	0.280
excludeDoubleMatchingProbes	0.012	0.000	0.009
exonStructure	11.313	0.032	11.350
findProbePositions	0.832	0.008	0.839
findSequenceInGenome	0.240	0.004	0.241
geneRegionScan	73.472	14.904	88.406
getLocalMetaprobeIntensities	0.000	0.008	0.008
getLocalProbeIntensities	0.000	0.008	0.006
getMetaprobesetsFromRegionOfInterest	0.000	0.008	0.007
getProbeLevelAnnotationForExonArrays	0.000	0.008	0.006
getProbesetsFromMetaprobeset	0.000	0.008	0.006
getProbesetsFromRegionOfInterest	0.000	0.008	0.006
getSequence	0.016	0.012	0.029
getServerProbeIntensities	0.008	0.020	0.028
plotCoexpression	51.780	15.381	67.162
plotOnGene	18.549	0.004	18.554
readGeneInput	0.004	0.000	0.005
translateSampleNames	0.064	0.000	0.067