BioC 2.14: CHECK report for GeneRegionScan on petty

Package: GeneRegionScan

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.20.0.tar.gz

StartedAt: 2014-10-07 22:09:16 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:16:50 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 454.2 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/GeneRegionScan.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.20.0’
* 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 ... [18s/18s] 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘Biostrings’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
readFASTA_replacement: no visible global function definition for
  ‘read.DNAStringSet’
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 files in ‘vignettes’ ... OK
* checking examples ... [245s/248s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
geneRegionScan   108.352  0.459 110.637
plotCoexpression  77.564  0.164  78.311
plotOnGene        26.254  0.110  26.453
exonStructure     16.609  0.093  16.856
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.001	0.000	0.001
checkForFileInPath	0.023	0.007	0.098
doProbeLinear	4.763	0.039	4.901
doProbeTTest	0.922	0.015	0.960
exampleProbeLevelSet	0.053	0.016	0.070
excludeDoubleMatchingProbes	0.001	0.000	0.001
exonStructure	16.609	0.093	16.856
findProbePositions	0.857	0.020	0.884
findSequenceInGenome	0.001	0.000	0.001
geneRegionScan	108.352	0.459	110.637
getLocalMetaprobeIntensities	0.002	0.000	0.001
getLocalProbeIntensities	0.002	0.001	0.002
getMetaprobesetsFromRegionOfInterest	0.001	0.000	0.002
getProbeLevelAnnotationForExonArrays	0.001	0.001	0.002
getProbesetsFromMetaprobeset	0.001	0.000	0.002
getProbesetsFromRegionOfInterest	0.001	0.000	0.002
getSequence	0.054	0.009	0.065
getServerProbeIntensities	0.001	0.000	0.001
plotCoexpression	77.564	0.164	78.311
plotOnGene	26.254	0.110	26.453
readGeneInput	0.002	0.000	0.002
translateSampleNames	0.104	0.004	0.108