Package: GeneRegionScan

Version: 1.14.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings GeneRegionScan_1.14.0.tar.gz

StartedAt: 2013-03-25 01:25:13 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:30:30 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 317.6 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/GeneRegionScan.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.14.0’
* 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 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
readGeneInput: warning in readFASTA(gene, strip.desc = FALSE): partial
  argument match of 'strip.desc' to 'strip.descs'
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   70.536 14.688  87.145
plotCoexpression 50.119 14.161  65.272
plotOnGene       17.598  0.008  17.809
exonStructure    12.957  0.016  13.222
* 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-2.11-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	0	0
checkForFileInPath	0.032	0.004	0.083
doProbeLinear	2.808	0.016	2.835
doProbeTTest	0.696	0.008	0.814
exampleProbeLevelSet	0.020	0.008	0.056
excludeDoubleMatchingProbes	0.000	0.000	0.001
exonStructure	12.957	0.016	13.222
findProbePositions	0.812	0.000	0.827
findSequenceInGenome	0	0	0
geneRegionScan	70.536	14.688	87.145
getLocalMetaprobeIntensities	0	0	0
getLocalProbeIntensities	0.004	0.000	0.000
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0	0	0
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0.000	0.000	0.001
getSequence	0.016	0.004	0.021
getServerProbeIntensities	0	0	0
plotCoexpression	50.119	14.161	65.272
plotOnGene	17.598	0.008	17.809
readGeneInput	0	0	0
translateSampleNames	0.060	0.000	0.071