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CHECK report for Genominator on merida2

This page was generated on 2019-04-09 13:25:02 -0400 (Tue, 09 Apr 2019).

Package 653/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Genominator 1.37.0
James Bullard
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Genominator
Branch: master
Last Commit: 9f8597c
Last Changed Date: 2018-10-30 11:54:28 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: Genominator
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Genominator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Genominator_1.37.0.tar.gz
StartedAt: 2019-04-09 01:09:08 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:12:04 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 175.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Genominator.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Genominator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Genominator_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Genominator.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.37.0’
* 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 ‘Genominator’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 to packages already attached by Depends:
  ‘GenomeGraphs’ ‘IRanges’
  Please remove these calls from your code.
'library' or 'require' call to ‘ShortRead’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenomeGraphs’ ‘RSQLite’
  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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.genominator.coverage plot.genominator.goodness.of.fit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
  ‘varLabels’
addPrimingWeights: no visible global function definition for
  ‘alignData’
addPrimingWeights: no visible global function definition for ‘subseq’
addPrimingWeights: no visible global function definition for ‘sread’
addPrimingWeights: no visible global function definition for
  ‘AlignedDataFrame’
addPrimingWeights: no visible global function definition for ‘pData’
addPrimingWeights: no visible global function definition for
  ‘varMetadata’
computePrimingWeights: no visible global function definition for
  ‘mkAllStrings’
computePrimingWeights : p.compute: no visible global function
  definition for ‘tables’
computePrimingWeights : p.compute: no visible global function
  definition for ‘subseq’
computePrimingWeights : p.compute: no visible global function
  definition for ‘sread’
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for ‘varLabels’
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for ‘alignData’
importFromAlignedReads : importObject: no visible global function
  definition for ‘position’
importFromAlignedReads : importObject: no visible global function
  definition for ‘chromosome’
importFromAlignedReads : importObject: no visible global function
  definition for ‘varLabels’
importFromAlignedReads : importObject: no visible global function
  definition for ‘alignData’
importFromAlignedReads: no visible global function definition for
  ‘readAligned’
makeAnnoFactory: no visible global function definition for
  ‘DisplayPars’
makeAnnoFactory : regionAnno.Biomart: no visible global function
  definition for ‘geneRegionBiomart’
makeAnnoFactory : regionAnno.AnnoData: no visible global function
  definition for ‘makeAnnotationTrack’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘DisplayPars’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for ‘makeBaseTrack’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for ‘makeGenericArray’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘makeGenomeAxis’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘gdPlot’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qchisq’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘ppoints’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qunif’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qqplot’
Undefined global functions or variables:
  AlignedDataFrame DisplayPars alignData chromosome gdPlot
  geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
  makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot
  qunif readAligned sread subseq tables varLabels varMetadata
Consider adding
  importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif")
to your NAMESPACE file.
* 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
joinExpData               11.416  0.038  11.580
addPrimingWeights          8.462  0.370   8.913
plot.genominator.coverage  6.273  0.080   6.424
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/Genominator.Rcheck/00check.log’
for details.



Installation output

Genominator.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Genominator
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Genominator’ ...
** R
** data
** 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 (Genominator)

Tests output


Example timings

Genominator.Rcheck/Genominator-Ex.timings

nameusersystemelapsed
ExpData0.0010.0000.002
addPrimingWeights8.4620.3708.913
aggregateExpData4.7500.0234.849
applyMapped2.7850.0332.862
collapseExpData3.6980.0693.795
computeCoverage2.1380.0272.204
computePrimingWeights0.3890.0120.406
getRegion0.6260.0020.639
importFromAlignedReads000
importToExpData1.3620.0051.384
joinExpData11.416 0.03811.580
makeGeneRepresentation0.2120.0040.216
mergeWithAnnotation1.4060.0111.425
plot.genominator.coverage6.2730.0806.424
plot.genominator.goodness.of.fit1.5230.0331.572
regionGoodnessOfFit-methods1.5030.0251.541
splitByAnnotation2.6650.0132.703
summarizeByAnnotation1.3600.0091.383
summarizeExpData1.3380.0061.352
validAnnotation0.0260.0040.030
yeastAnno0.2130.0160.231