BioC 2.14: CHECK report for GeneRegionScan on moscato2

Package: GeneRegionScan

Version: 1.20.0

Command: rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.20.0.tar.gz >GeneRegionScan-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.20.0.tar.gz

StartedAt: 2014-10-08 01:25:08 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:31:29 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 381.8 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.20.0.tar.gz >GeneRegionScan-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.20.0.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/GeneRegionScan.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [112s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   50.25   0.04   50.31
plotCoexpression 34.63   0.00   34.65
plotOnGene       11.50   0.00   11.50
exonStructure     7.85   0.00    7.84
** running examples for arch 'x64' ... [130s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   57.61   0.03   57.67
plotCoexpression 42.01   0.00   42.01
plotOnGene       14.34   0.03   14.37
exonStructure     8.52   0.00    8.52
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'GeneRegionScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneRegionScan' as GeneRegionScan_1.20.0.zip
* DONE (GeneRegionScan)

name	user	system	elapsed
addSnpPdata	0	0	0
checkForFileInPath	0.08	0.01	0.33
doProbeLinear	2.05	0.02	2.06
doProbeTTest	0.39	0.00	0.39
exampleProbeLevelSet	0.11	0.00	0.11
excludeDoubleMatchingProbes	0	0	0
exonStructure	7.85	0.00	7.84
findProbePositions	0.39	0.00	0.39
findSequenceInGenome	0	0	0
geneRegionScan	50.25	0.04	50.31
getLocalMetaprobeIntensities	0	0	0
getLocalProbeIntensities	0	0	0
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0	0	0
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0	0	0
getSequence	0.02	0.00	0.01
getServerProbeIntensities	0.01	0.00	0.02
plotCoexpression	34.63	0.00	34.65
plotOnGene	11.5	0.0	11.5
readGeneInput	0	0	0
translateSampleNames	0.06	0.00	0.06

name	user	system	elapsed
addSnpPdata	0	0	0
checkForFileInPath	0.03	0.02	0.05
doProbeLinear	2.31	0.00	2.31
doProbeTTest	0.43	0.01	0.45
exampleProbeLevelSet	0.02	0.00	0.02
excludeDoubleMatchingProbes	0.01	0.00	0.01
exonStructure	8.52	0.00	8.52
findProbePositions	0.50	0.02	0.52
findSequenceInGenome	0	0	0
geneRegionScan	57.61	0.03	57.67
getLocalMetaprobeIntensities	0	0	0
getLocalProbeIntensities	0	0	0
getMetaprobesetsFromRegionOfInterest	0	0	0
getProbeLevelAnnotationForExonArrays	0	0	0
getProbesetsFromMetaprobeset	0	0	0
getProbesetsFromRegionOfInterest	0	0	0
getSequence	0.03	0.00	0.03
getServerProbeIntensities	0	0	0
plotCoexpression	42.01	0.00	42.01
plotOnGene	14.34	0.03	14.37
readGeneInput	0.02	0.00	0.02
translateSampleNames	0.09	0.00	0.09