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CHECK report for GeneRegionScan on merida1

This page was generated on 2021-05-06 12:35:05 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GeneRegionScan package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 697/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneRegionScan 1.46.0  (landing page)
Lasse Folkersen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GeneRegionScan
Branch: RELEASE_3_12
Last Commit: 43d8744
Last Changed Date: 2020-10-27 10:35:37 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GeneRegionScan
Version: 1.46.0
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_1.46.0.tar.gz
StartedAt: 2021-05-06 02:03:25 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:06:36 -0400 (Thu, 06 May 2021)
EllapsedTime: 190.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneRegionScan.Rcheck
Warnings: 0

Command output

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### 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_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/GeneRegionScan.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneRegionScan/DESCRIPTION’ ... OK
* this is package ‘GeneRegionScan’ version ‘1.46.0’
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
geneRegionScan   39.545  0.275  39.871
plotCoexpression 28.571  0.111  28.714
plotOnGene       10.851  0.065  10.995
exonStructure     7.119  0.055   7.184
* 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-3.12-bioc/meat/GeneRegionScan.Rcheck/00check.log’
for details.



Installation output

GeneRegionScan.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneRegionScan
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneRegionScan’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneRegionScan)

Tests output


Example timings

GeneRegionScan.Rcheck/GeneRegionScan-Ex.timings

nameusersystemelapsed
addSnpPdata0.0000.0000.001
checkForFileInPath0.0110.0110.024
doProbeLinear1.8650.0851.952
doProbeTTest0.3820.0110.394
exampleProbeLevelSet0.0360.0220.059
excludeDoubleMatchingProbes0.0000.0010.000
exonStructure7.1190.0557.184
findProbePositions0.5040.0110.516
findSequenceInGenome0.0000.0000.001
geneRegionScan39.545 0.27539.871
getLocalMetaprobeIntensities0.0000.0000.001
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest0.0000.0000.001
getProbeLevelAnnotationForExonArrays0.0000.0000.001
getProbesetsFromMetaprobeset0.0000.0000.001
getProbesetsFromRegionOfInterest0.0010.0010.001
getSequence0.0290.0140.044
getServerProbeIntensities0.0000.0000.001
plotCoexpression28.571 0.11128.714
plotOnGene10.851 0.06510.995
readGeneInput0.0010.0010.001
translateSampleNames0.0550.0040.058