Package: GeneRegionScan

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneRegionScan_1.36.0.tar.gz

StartedAt: 2018-10-16 21:36:21 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:39:13 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 171.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneRegionScan.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneRegionScan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneRegionScan_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneRegionScan.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.36.0’
* 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 ... 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
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘BSgenome’ ‘affy’
  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
createFeatureData: no visible global function definition for ‘new’
exonStructure: no visible global function definition for ‘lines’
exonStructure: no visible global function definition for ‘points’
exonStructure: no visible global function definition for ‘text’
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’
getLocalMetaprobeIntensities: no visible global function definition for
  ‘read.table’
getLocalMetaprobeIntensities: no visible global function definition for
  ‘new’
getLocalProbeIntensities: no visible global function definition for
  ‘read.table’
getLocalProbeIntensities : get_probe_indices: no visible global
  function definition for ‘xy2indices’
getLocalProbeIntensities: no visible global function definition for
  ‘new’
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
  ‘read.table’
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’
doProbeLinear,ExpressionSet: no visible global function definition for
  ‘lm’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘pData’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘featureNames’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘t.test’
doProbeTTest,ExpressionSet: no visible global function definition for
  ‘wilcox.test’
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 ‘startIndex’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘pdf’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘split.screen’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘screen’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘par’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘close.screen’
geneRegionScan,ExpressionSet: no visible global function definition for
  ‘dev.off’
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: no visible global function definition
  for ‘frame’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘plot.window’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘lines’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘text’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘combn’
plotCoexpression,ExpressionSet : calculate_coexpression: no visible
  global function definition for ‘featureNames’
plotCoexpression,ExpressionSet : calculate_coexpression: no visible
  global function definition for ‘cor.test’
plotCoexpression,ExpressionSet: no visible global function definition
  for ‘points’
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 binding for global variable
  ‘median’
plotOnGene,ExpressionSet: no visible binding for global variable
  ‘quantile’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘plot.default’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘mtext’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘experimentData’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘median’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘quantile’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘lines’
plotOnGene,ExpressionSet: no visible global function definition for
  ‘points’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘pData’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘mtext’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘median’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘quantile’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘lines’
plotStatistics,ExpressionSet: no visible global function definition for
  ‘text’
translateSampleNames,ExpressionSet: no visible global function
  definition for ‘read.table’
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<-’
Undefined global functions or variables:
  close.screen combn cor.test dev.off experimentData exprs<-
  featureData featureData<- featureNames frame interval lines lm median
  mtext new notes notes<- pData pData<- par pdf plot.default
  plot.window points quantile read.DNAStringSet read.table reverse
  revmap sampleNames screen seqnames split.screen startIndex t.test
  text unmasked wilcox.test xy2indices
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "close.screen", "frame", "lines", "mtext",
             "par", "plot.default", "plot.window", "points", "screen",
             "split.screen", "text")
  importFrom("methods", "new")
  importFrom("stats", "cor.test", "lm", "median", "quantile", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
geneRegionScan   38.703  0.247  39.174
plotCoexpression 27.901  0.079  28.234
plotOnGene        9.475  0.047   9.610
exonStructure     5.666  0.071   5.756
* 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

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneRegionScan.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneRegionScan
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GeneRegionScan’ ...
** R
** data
** exec
** inst
** byte-compile and prepare 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	0.002	0.000	0.002
checkForFileInPath	0.011	0.005	0.016
doProbeLinear	1.935	0.083	2.024
doProbeTTest	0.362	0.009	0.372
exampleProbeLevelSet	0.035	0.011	0.047
excludeDoubleMatchingProbes	0.002	0.000	0.002
exonStructure	5.666	0.071	5.756
findProbePositions	0.258	0.004	0.262
findSequenceInGenome	0.002	0.000	0.001
geneRegionScan	38.703	0.247	39.174
getLocalMetaprobeIntensities	0.001	0.000	0.002
getLocalProbeIntensities	0.001	0.000	0.001
getMetaprobesetsFromRegionOfInterest	0.002	0.000	0.002
getProbeLevelAnnotationForExonArrays	0.001	0.000	0.001
getProbesetsFromMetaprobeset	0.002	0.001	0.003
getProbesetsFromRegionOfInterest	0.001	0.000	0.001
getSequence	0.024	0.005	0.029
getServerProbeIntensities	0.002	0.000	0.001
plotCoexpression	27.901	0.079	28.234
plotOnGene	9.475	0.047	9.610
readGeneInput	0.003	0.000	0.004
translateSampleNames	0.040	0.003	0.042