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CHECK report for IdMappingAnalysis on merida2

This page was generated on 2018-10-17 08:50:20 -0400 (Wed, 17 Oct 2018).

Package 718/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.24.0
Alex Lisovich , Roger Day
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: RELEASE_3_7
Last Commit: 7a8f4be
Last Changed Date: 2018-04-30 10:35:24 -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: IdMappingAnalysis
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IdMappingAnalysis_1.24.0.tar.gz
StartedAt: 2018-10-16 22:03:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:04:17 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 75.3 seconds
RetCode: 0
Status:  OK 
CheckDir: IdMappingAnalysis.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings IdMappingAnalysis_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/IdMappingAnalysis.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 ‘IdMappingAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingAnalysis’ version ‘1.24.0’
* 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 ‘IdMappingAnalysis’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘R.oo’ ‘rChoiceDialogs’
  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
.onAttach: no visible global function definition for
  ‘packageDescription’
Bootstrap: no visible global function definition for ‘extend’
Bootstrap : FUN: no visible global function definition for ‘cor’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
Corr: no visible global function definition for ‘cor’
CorrData: no visible global function definition for ‘extend’
CorrData: no visible global function definition for ‘Object’
DataFilter: no visible global function definition for ‘extend’
DataFilter: no visible global function definition for ‘Object’
Display: no visible global function definition for ‘extend’
Display: no visible global function definition for ‘Object’
IdMap: no visible global function definition for ‘throw’
IdMap: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘throw’
IdMapBase: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘Object’
IdMapCounts: no visible global function definition for ‘throw’
IdMapCounts: no visible global function definition for ‘extend’
IdMapDiff: no visible global function definition for ‘throw’
IdMapDiff: no visible global function definition for ‘extend’
IdMapDiffCounts: no visible global function definition for ‘extend’
JointIdMap: no visible global function definition for ‘extend’
JointUniquePairs: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘Object’
Mixture: no visible global function definition for ‘extend’
Mixture: no visible global function definition for ‘Object’
Mixture: no visible global function definition for ‘density’
Mixture : <anonymous>: no visible global function definition for
  ‘dnorm’
Subset: no visible global function definition for ‘extend’
Subset: no visible global function definition for ‘Object’
UniquePairs: no visible global function definition for ‘throw’
UniquePairs: no visible global function definition for ‘extend’
as.IdMap.UniquePairs: no visible global function definition for
  ‘getName’
as.MultiSet.CorrData: no visible global function definition for ‘new’
as.data.frame.IdMapBase: no visible global function definition for
  ‘getName’
as.data.frame.IdMapBase: no visible global function definition for
  ‘throw’
as.data.frame.IdMapBase: no visible global function definition for ‘as’
as.list.IdMap: no visible global function definition for ‘throw’
boxplot.JointUniquePairs: no visible global function definition for
  ‘par’
boxplot.JointUniquePairs: no visible global function definition for
  ‘axis’
boxplot.JointUniquePairs: no visible global function definition for
  ‘text’
boxplotdataJitter.JointUniquePairs: no visible global function
  definition for ‘par’
copy.Display: no visible global function definition for ‘dev.cur’
copy.Display: no visible global function definition for ‘par’
copy.Display: no visible global function definition for ‘png’
copy.Display: no visible global function definition for ‘jpeg’
copy.Display: no visible global function definition for ‘tiff’
copy.Display: no visible global function definition for ‘bmp’
copy.Display: no visible global function definition for ‘pdf’
copy.Display: no visible global function definition for ‘dev.set’
copy.Display: no visible global function definition for ‘dev.copy’
copy.Display: no visible global function definition for ‘dev.next’
copy.Display: no visible global function definition for ‘dev.off’
corr.boxplot.JointUniquePairs: no visible global function definition
  for ‘boxplot’
corr.boxplot.JointUniquePairs: no visible global function definition
  for ‘abline’
create.Display: no visible global function definition for ‘dev.new’
create.Display: no visible global function definition for ‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘plot’
ecdf.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
ecdf.plot.JointIdMap: no visible global function definition for ‘par’
ecdf.plot.JointIdMap: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘rbinom’
fit2clusters: no visible global function definition for ‘rgamma’
fit2clusters: no visible global function definition for ‘rnorm’
fit2clusters: no visible global function definition for ‘dnorm’
fit2clusters: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘lines’
fit2clusters: no visible global function definition for ‘density’
fit2clusters: no visible global function definition for ‘legend’
fit2clusters: no visible global function definition for ‘par’
getCorr.JointUniquePairs: no visible global function definition for
  ‘equals’
getExperimentSet.CorrData: no visible global function definition for
  ‘throw’
getExperimentSet.CorrData: no visible global function definition for
  ‘new’
getIdMapList.JointIdMap: no visible global function definition for
  ‘throw’
interactive.plot.CorrData: no visible global function definition for
  ‘rselect.list’
interactive.plot.CorrData: no visible global function definition for
  ‘plot’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘par’
line.loess.Display: no visible global function definition for ‘loess’
line.loess.Display: no visible global function definition for ‘lines’
line.unsorted.Display: no visible global function definition for
  ‘lines’
merge.IdMap: no visible global function definition for ‘getName’
mixture.boxplot.JointUniquePairs: no visible global function definition
  for ‘boxplot’
mixture.boxplot.JointUniquePairs: no visible global function definition
  for ‘abline’
mixture.plot.JointUniquePairs: no visible global function definition
  for ‘plot’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for ‘par’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for ‘legend’
plot.Corr: no visible global function definition for ‘density’
plot.Corr: no visible global function definition for ‘plot.new’
plot.Corr: no visible global function definition for ‘plot.window’
plot.Corr: no visible global function definition for ‘axis’
plot.Corr: no visible global function definition for ‘par’
plot.Corr: no visible global function definition for ‘box’
plot.Corr: no visible global function definition for ‘lines’
plot.Corr: no visible global function definition for ‘legend’
plot.Corr: no visible global function definition for ‘abline’
plot.CorrData: no visible global function definition for ‘cor’
plot.CorrData: no visible global function definition for ‘par’
plot.CorrData: no visible global function definition for ‘plot’
plot.CorrData: no visible global function definition for ‘box’
plot.CorrData: no visible global function definition for ‘axis’
plot.CorrData: no visible global function definition for ‘points’
plot.CorrData: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘plot.new’
plot.IdMapCounts: no visible global function definition for
  ‘plot.window’
plot.IdMapCounts: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘axis’
plot.IdMapCounts: no visible global function definition for ‘par’
plot.IdMapCounts: no visible global function definition for ‘box’
plot.IdMapCounts: no visible global function definition for ‘ecdf’
plot.IdMapCounts: no visible global function definition for ‘lines’
plot.IdMapCounts: no visible global function definition for ‘legend’
plot.IdMapDiffCounts : plotValGroup: no visible global function
  definition for ‘rect’
plot.IdMapDiffCounts: no visible global function definition for
  ‘plot.new’
plot.IdMapDiffCounts: no visible global function definition for ‘par’
plot.IdMapDiffCounts: no visible global function definition for
  ‘plot.window’
plot.IdMapDiffCounts: no visible global function definition for ‘title’
plot.IdMapDiffCounts: no visible global function definition for ‘axis’
plot.IdMapDiffCounts: no visible global function definition for ‘mtext’
plot.IdMapDiffCounts: no visible global function definition for ‘lines’
plot.IdMapDiffCounts: no visible global function definition for ‘text’
plot.IdMapDiffCounts: no visible global function definition for
  ‘abline’
plot.Mixture: no visible global function definition for ‘plot.new’
plot.Mixture: no visible global function definition for ‘plot.window’
plot.Mixture: no visible global function definition for ‘axis’
plot.Mixture: no visible global function definition for ‘par’
plot.Mixture: no visible global function definition for ‘box’
plot.Mixture: no visible global function definition for ‘lines’
plot.Mixture: no visible global function definition for ‘density’
plot.Mixture: no visible global function definition for ‘rug’
plot.Mixture: no visible global function definition for ‘dnorm’
plot.Mixture : <anonymous>: no visible global function definition for
  ‘dnorm’
plot.Mixture: no visible global function definition for ‘legend’
plot.Mixture: no visible global function definition for ‘abline’
progressMsg.Display: no visible global function definition for
  ‘flush.console’
textBoundingBox.Display: no visible global function definition for
  ‘strwidth’
textBoundingBox.Display: no visible global function definition for
  ‘strheight’
textBoundingBox.Display: no visible global function definition for
  ‘par’
to.index.expr.Misc: no visible global function definition for ‘tail’
unique.UniquePairs: no visible global function definition for ‘getName’
zoom.pars.Display: no visible global function definition for ‘par’
Undefined global functions or variables:
  Object abline as axis bmp box boxplot cor density dev.copy dev.cur
  dev.new dev.next dev.off dev.set dnorm ecdf equals extend
  flush.console getName jpeg legend lines loess mtext new
  packageDescription par pdf plot plot.new plot.window png points
  rbinom rect rgamma rnorm rselect.list rug strheight strwidth tail
  text throw tiff title
Consider adding
  importFrom("grDevices", "bmp", "dev.copy", "dev.cur", "dev.new",
             "dev.next", "dev.off", "dev.set", "jpeg", "pdf", "png",
             "tiff")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
             "lines", "mtext", "par", "plot", "plot.new", "plot.window",
             "points", "rect", "rug", "strheight", "strwidth", "text",
             "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "cor", "density", "dnorm", "ecdf", "loess",
             "rbinom", "rgamma", "rnorm")
  importFrom("utils", "flush.console", "packageDescription", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: DataFilter.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Display.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Misc.Rd:41-42: Dropping empty section \arguments
* 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 ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
getBootstrap.JointUniquePairs 7.12  0.061   7.232
Bootstrap                     6.68  0.088   6.822
* 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/IdMappingAnalysis.Rcheck/00check.log’
for details.



Installation output

IdMappingAnalysis.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL IdMappingAnalysis
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘IdMappingAnalysis’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘IdMappingAnalysis.Rnw’ using ‘latin-9’ 
** testing if installed package can be loaded
* DONE (IdMappingAnalysis)

Tests output


Example timings

IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings

nameusersystemelapsed
000-LB-.IdMapBase0.0850.0160.102
Bootstrap6.6800.0886.822
Corr0.4160.0140.435
CorrData0.0430.0010.044
CsvList.merge.Misc0.0020.0000.002
IdMap0.0080.0000.008
IdMapBase0.0020.0000.003
IdMapCounts0.2930.0140.313
IdMapDiff0.3950.0090.411
IdMapDiffCounts0.3910.0040.403
JointIdMap0.0790.0030.085
JointUniquePairs0.5870.0070.603
Mixture0.1780.0010.182
UniquePairs0.0030.0000.003
aligned.IdMapBase0.0060.0000.005
as.IdMap.UniquePairs0.0290.0000.029
as.MultiSet.CorrData0.490.010.50
as.UniquePairs.IdMap0.0280.0000.029
as.data.frame.IdMapBase0.1050.0010.105
as.data.frame.JointIdMap0.0510.0050.056
as.list.IdMap0.0080.0000.009
boxplot.JointUniquePairs0.0560.0040.059
byColNames.Subset0.0060.0000.013
byColumn.Subset0.0050.0000.005
byRow.Subset0.0040.0000.005
byRowNames.Subset0.0050.0000.006
clust.Mixture0.0010.0000.002
copy.Display0.0020.0000.002
corr.boxplot.JointUniquePairs0.0960.0010.101
corr.plot.JointUniquePairs0.0580.0010.061
create.Display0.0010.0000.002
create.UniquePairs0.1190.0010.121
diffCounts.plot.JointIdMap0.5070.0040.522
dim.IdMapBase0.0030.0000.003
dimnames.IdMapBase0.0030.0000.004
do.glm.JointUniquePairs0.0120.0000.012
ecdf.plot.JointIdMap0.1730.0020.176
equals.UniquePairs0.0440.0000.044
fisherTransform.DataFilter0.0020.0000.002
fisherTransformInverse.DataFilter0.0010.0000.002
fisherTransformJacobean.DataFilter0.0020.0010.002
getBootstrap.JointUniquePairs7.1200.0617.232
getCompoundEvents.IdMapDiffCounts0.3530.0050.358
getCompoundGroups.IdMapDiffCounts0.3610.0050.365
getCorr.JointUniquePairs0.0390.0010.042
getCorrData.JointUniquePairs0.0360.0010.037
getCorrDataFrame.JointUniquePairs0.0140.0010.014
getCounts.IdMap0.0230.0000.022
getCounts.JointIdMap0.1580.0020.162
getData.Corr0.0010.0000.002
getData.Mixture0.0040.0000.005
getDiff.JointIdMap0.2020.0040.208
getExperimentSet.CorrData0.0920.0040.096
getIdMapList.JointIdMap0.0690.0010.070
getMapNames.JointIdMap0.0710.0040.075
getMapNames.JointUniquePairs0.0030.0000.003
getMatch.UniquePairs0.0530.0010.054
getMatchInfo.JointIdMap0.0760.0030.079
getMatchInfo.JointUniquePairs0.3770.0000.380
getMixture.JointUniquePairs0.1520.0020.156
getSampleNames.CorrData0.0040.0010.004
getStats.IdMapCounts0.1690.0030.175
getStats.Mixture0.0030.0000.003
getUnionIdMap.JointIdMap0.4680.0050.474
getUniquePairs.Corr0.0060.0000.006
getUniquePairs.CorrData0.0050.0000.006
getUniquePairs.JointUniquePairs0.0040.0000.004
interactive.corr.boxplot.JointUniquePairs0.0700.0010.071
interactive.corr.plot.JointUniquePairs0.0500.0050.054
interactive.mixture.boxplot.JointUniquePairs0.1930.0060.199
interactive.mixture.plot.JointUniquePairs0.1320.0060.140
interactive.plot.CorrData0.0360.0010.037
interactive.plot.JointUniquePairs0.0020.0000.002
interleave.Misc0.0010.0000.002
line.loess.Display0.0010.0000.002
line.unsorted.Display0.0010.0000.001
logTen.DataFilter0.0750.0040.080
merge.IdMap0.6710.0040.682
minAvgCountConstraint.DataFilter0.0940.0030.099
minCountConstraint.DataFilter0.1250.0080.135
minCountGroupConstraint.DataFilter0.1420.0070.151
mixture.boxplot.JointUniquePairs0.2100.0040.216
mixture.plot.JointUniquePairs0.1440.0020.149
plot.Bootstrap0.0800.0010.082
plot.Corr0.0500.0010.053
plot.CorrData0.0290.0000.030
plot.IdMapCounts0.1460.0010.151
plot.IdMapDiffCounts0.6240.0030.633
plot.Mixture0.0150.0010.016
primaryIDs.IdMapBase0.0050.0010.005
primaryKey.CorrData0.0020.0000.002
primaryKey.IdMapBase0.0040.0000.004
primaryKey.Mixture0.0020.0000.002
progressMsg.Display0.0020.0000.002
removeNASeries.DataFilter0.1270.0080.137
secondaryKey.CorrData0.0020.0000.003
secondaryKey.IdMapBase0.0040.0010.003
secondaryKey.Mixture0.0020.0000.002
subsetCorr.JointUniquePairs0.0150.0010.015
subsetData.JointUniquePairs0.0080.0000.008
subsetGroups.JointUniquePairs0.6780.0080.690
summary.IdMapDiffCounts0.3670.0010.373
swapKeys.IdMap0.0490.0010.050
swapKeys.UniquePairs0.0250.0010.026
textBoundingBox.Display0.0020.0000.002
to.base.Misc0.0020.0000.002
to.binary.logical.Misc0.0030.0000.003
to.index.expr.Misc0.0010.0010.001
unique.UniquePairs0.0530.0000.054
words.Misc0.0020.0000.003
zoom.pars.Display0.0010.0000.001