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BioC 3.0: CHECK report for GeneRegionScan on perceval

This page was generated on 2015-04-10 09:54:28 -0700 (Fri, 10 Apr 2015).

Package 354/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneRegionScan 1.22.0
Lasse Folkersen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GeneRegionScan
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: GeneRegionScan
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.22.0.tar.gz
StartedAt: 2015-04-10 01:54:39 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:59:42 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 303.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GeneRegionScan.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneRegionScan_1.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneRegionScan.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.22.0’
* 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 ... [14s/19s] 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
'library' or 'require' calls in package code:
  ‘affy’ ‘AnnotationDbi’ ‘BSgenome’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* 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'
exonStructure: no visible global function definition for ‘width’
findSequenceInGenome: no visible global function definition for
  ‘seqnames’
findSequenceInGenome: no visible global function definition for
  ‘reverse’
findSequenceInGenome: no visible global function definition for
  ‘unmasked’
findSequenceInGenome: no visible global function definition for
  ‘startIndex’
getLocalProbeIntensities : get_probe_indices: no visible global
  function definition for ‘xy2indices’
getProbesetsFromRegionOfInterest: no visible global function definition
  for ‘revmap’
readFASTA_replacement: no visible global function definition for
  ‘read.DNAStringSet’
addSnpPdata,ExpressionSet: no visible global function definition for
  ‘sampleNames’
addSnpPdata,ExpressionSet: no visible global function definition for
  ‘pData’
addSnpPdata,ExpressionSet: no visible global function definition for
  ‘pData<-’
addSnpPdata,ExpressionSet: no visible global function definition for
  ‘notes’
addSnpPdata,ExpressionSet: no visible global function definition for
  ‘notes<-’
doProbeLinear,ExpressionSet: no visible global function definition for
  ‘pData’
doProbeLinear,ExpressionSet: no visible global function definition for
  ‘featureNames’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘pData’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘featureNames’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘featureNames’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘pData’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘featureData’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘pData<-’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘featureData<-’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘exprs<-’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘notes’
excludeDoubleMatchingProbes,ProbeLevelSet: no visible global function
  definition for ‘notes<-’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘pData’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘featureData’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘featureNames’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘reverse’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘countIndex’
findProbePositions,ExpressionSet: no visible global function definition
  for ‘startIndex’
getSequence,ProbeLevelSet: no visible global function definition for
  ‘pData’
getSequence,ProbeLevelSet: no visible global function definition for
  ‘featureData’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘pData’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘featureData’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘featureNames’
plotCoexpression,ExpressionSet: no visible binding for global variable
  ‘interval’
plotCoexpression,ExpressionSet : calculate_coexpression: no visible
  global function definition for ‘featureNames’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘pData’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘pData<-’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘featureData’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘featureNames’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘experimentData’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘pData’
translateSampleNames,ExpressionSet: no visible global function
  definition for ‘sampleNames’
translateSampleNames,ExpressionSet: no visible global function
  definition for ‘pData’
translateSampleNames,ExpressionSet: no visible global function
  definition for ‘pData<-’
translateSampleNames,ExpressionSet: no visible global function
  definition for ‘exprs<-’
* 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 ... [130s/135s] WARNING
Found the following significant warnings:

  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
  Warning: 'countIndex' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   56.468  0.276  57.520
plotCoexpression 37.147  0.137  37.323
plotOnGene       14.962  0.050  15.045
exonStructure     9.578  0.073  13.435
* 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
* DONE

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/GeneRegionScan.Rcheck/00check.log’
for details.

GeneRegionScan.Rcheck/00install.out:

* 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)

GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings:

nameusersystemelapsed
addSnpPdata0.0010.0000.001
checkForFileInPath0.0150.0050.150
doProbeLinear2.6130.0242.640
doProbeTTest0.4410.0180.462
exampleProbeLevelSet0.0350.0150.050
excludeDoubleMatchingProbes0.0010.0000.001
exonStructure 9.578 0.07313.435
findProbePositions0.8420.0090.855
findSequenceInGenome0.0000.0010.001
geneRegionScan56.468 0.27657.520
getLocalMetaprobeIntensities0.0010.0010.001
getLocalProbeIntensities0.0010.0000.001
getMetaprobesetsFromRegionOfInterest0.0000.0000.001
getProbeLevelAnnotationForExonArrays0.0010.0000.001
getProbesetsFromMetaprobeset0.0010.0010.001
getProbesetsFromRegionOfInterest0.0010.0000.001
getSequence0.0360.0070.044
getServerProbeIntensities0.0010.0000.001
plotCoexpression37.147 0.13737.323
plotOnGene14.962 0.05015.045
readGeneInput0.0010.0000.001
translateSampleNames0.0560.0030.059