BioC 2.13: CHECK report for GeneRegionScan on perceval

Package: GeneRegionScan

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.18.0.tar.gz

StartedAt: 2014-04-05 01:31:47 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:37:49 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 361.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/GeneRegionScan.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.18.0’
* 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 ... [15s/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 ‘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 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘GeneRegionScan.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [198s/202s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   82.388  7.069  91.440
plotCoexpression 59.151  6.674  66.736
plotOnGene       19.349  0.179  19.712
exonStructure    11.827  0.124  12.249
* 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 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.007	0.001	0.009
checkForFileInPath	0.023	0.007	0.102
doProbeLinear	2.492	0.030	2.550
doProbeTTest	0.849	0.031	0.936
exampleProbeLevelSet	0.045	0.015	0.061
excludeDoubleMatchingProbes	0.008	0.001	0.009
exonStructure	11.827	0.124	12.249
findProbePositions	0.982	0.032	1.031
findSequenceInGenome	0.003	0.004	0.007
geneRegionScan	82.388	7.069	91.440
getLocalMetaprobeIntensities	0.003	0.005	0.008
getLocalProbeIntensities	0.003	0.005	0.008
getMetaprobesetsFromRegionOfInterest	0.002	0.004	0.007
getProbeLevelAnnotationForExonArrays	0.003	0.004	0.007
getProbesetsFromMetaprobeset	0.002	0.006	0.008
getProbesetsFromRegionOfInterest	0.002	0.006	0.008
getSequence	0.039	0.014	0.053
getServerProbeIntensities	0.004	0.008	0.012
plotCoexpression	59.151	6.674	66.736
plotOnGene	19.349	0.179	19.712
readGeneInput	0.003	0.005	0.009
translateSampleNames	0.082	0.016	0.098