BioC 2.12: CHECK report for GeneRegionScan on petty

Package: GeneRegionScan

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.16.0.tar.gz

StartedAt: 2013-10-08 22:30:39 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:38:12 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 453.0 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 3.0.1 (2013-05-16)
* 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 '1.16.0'
* 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 ... [17s/17s] 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 ... [273s/277s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneRegionScan   114.748  8.299 124.809
plotCoexpression  83.630  8.931  93.310
plotOnGene        26.938  0.156  27.725
exonStructure     16.354  0.134  17.096
* 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
** testing if installed package can be loaded
* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0.192	0.003	0.195
checkForFileInPath	0.022	0.006	0.076
doProbeLinear	3.664	0.044	3.724
doProbeTTest	0.786	0.032	0.820
exampleProbeLevelSet	0.048	0.016	0.063
excludeDoubleMatchingProbes	0.014	0.001	0.015
exonStructure	16.354	0.134	17.096
findProbePositions	0.822	0.026	0.850
findSequenceInGenome	0.003	0.003	0.007
geneRegionScan	114.748	8.299	124.809
getLocalMetaprobeIntensities	0.003	0.005	0.009
getLocalProbeIntensities	0.004	0.006	0.009
getMetaprobesetsFromRegionOfInterest	0.003	0.005	0.007
getProbeLevelAnnotationForExonArrays	0.003	0.005	0.008
getProbesetsFromMetaprobeset	0.003	0.005	0.008
getProbesetsFromRegionOfInterest	0.003	0.005	0.008
getSequence	0.027	0.015	0.041
getServerProbeIntensities	0.004	0.008	0.012
plotCoexpression	83.630	8.931	93.310
plotOnGene	26.938	0.156	27.725
readGeneInput	0.003	0.005	0.008
translateSampleNames	0.105	0.014	0.118