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CHECK report for Genominator on malbec2

This page was generated on 2018-10-17 08:22:55 -0400 (Wed, 17 Oct 2018).

Package 600/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Genominator 1.34.0
James Bullard
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Genominator
Branch: RELEASE_3_7
Last Commit: 2810142
Last Changed Date: 2018-04-30 10:35:12 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  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 UNNEEDED, same version exists in internal repository

Summary

Package: Genominator
Version: 1.34.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Genominator.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Genominator_1.34.0.tar.gz
StartedAt: 2018-10-16 00:46:23 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:48:15 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 112.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Genominator.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:Genominator.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings Genominator_1.34.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/Genominator.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.34.0’
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
joinExpData               10.416  0.004  10.426
addPrimingWeights          5.844  0.204   6.073
plot.genominator.coverage  5.448  0.028   5.483
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/Genominator.Rcheck/00check.log’
for details.



Installation output

Genominator.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL Genominator
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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
ExpData0.0000.0000.002
addPrimingWeights5.8440.2046.073
aggregateExpData3.8920.0043.897
applyMapped2.5720.0162.772
collapseExpData3.7840.0123.800
computeCoverage1.9440.0281.977
computePrimingWeights0.2320.0040.237
getRegion0.5280.0000.530
importFromAlignedReads0.0040.0000.000
importToExpData1.2880.0001.290
joinExpData10.416 0.00410.426
makeGeneRepresentation0.1320.0000.132
mergeWithAnnotation1.1880.0001.188
plot.genominator.coverage5.4480.0285.483
plot.genominator.goodness.of.fit1.2520.0081.261
regionGoodnessOfFit-methods1.2800.0041.286
splitByAnnotation2.4120.0082.422
summarizeByAnnotation1.1440.0041.150
summarizeExpData1.1440.0001.144
validAnnotation0.0160.0000.016
yeastAnno0.1320.0080.139