BioC 2.12: CHECK report for GeneRegionScan on george2

Package: GeneRegionScan

Version: 1.16.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GeneRegionScan_1.16.0.tar.gz

StartedAt: 2013-10-09 02:02:49 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:10:18 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 449.2 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GeneRegionScan.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.16.0’
* 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 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 ... [16s/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 ... [277s/279s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneRegionScan   101.731 26.841 129.993
plotCoexpression  68.652 24.730  93.719
plotOnGene        24.594  0.028  24.636
exonStructure     15.629  0.048  15.940
* 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
  ‘/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
** testing if installed package can be loaded
* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0.348	0.000	0.347
checkForFileInPath	0.032	0.000	0.042
doProbeLinear	3.328	0.020	3.348
doProbeTTest	1.068	0.004	1.073
exampleProbeLevelSet	0.040	0.012	0.053
excludeDoubleMatchingProbes	0.016	0.000	0.013
exonStructure	15.629	0.048	15.940
findProbePositions	1.324	0.016	1.508
findSequenceInGenome	0.004	0.004	0.015
geneRegionScan	101.731	26.841	129.993
getLocalMetaprobeIntensities	0.000	0.012	0.011
getLocalProbeIntensities	0.000	0.016	0.013
getMetaprobesetsFromRegionOfInterest	0.000	0.012	0.010
getProbeLevelAnnotationForExonArrays	0.000	0.012	0.010
getProbesetsFromMetaprobeset	0.000	0.008	0.010
getProbesetsFromRegionOfInterest	0.004	0.004	0.010
getSequence	0.012	0.028	0.041
getServerProbeIntensities	0.008	0.012	0.017
plotCoexpression	68.652	24.730	93.719
plotOnGene	24.594	0.028	24.636
readGeneInput	0.008	0.000	0.009
translateSampleNames	0.092	0.004	0.095