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CHECK report for IdMappingAnalysis on merida2

This page was generated on 2019-04-09 13:26:56 -0400 (Tue, 09 Apr 2019).

Package 783/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.27.0
Alex Lisovich , Roger Day
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: master
Last Commit: c5369b9
Last Changed Date: 2018-10-30 11:54:30 -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  OK  OK  OK UNNEEDED, same version exists in internal repository
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: IdMappingAnalysis
Version: 1.27.0
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_1.27.0.tar.gz
StartedAt: 2019-04-09 01:35:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:37:23 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 100.7 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_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IdMappingAnalysis.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 ‘IdMappingAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingAnalysis’ version ‘1.27.0’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  boxplot.JointUniquePairs getName.IdMapBase primaryKey.IdMapBase
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
.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 7.851  0.145   8.072
Bootstrap                     6.814  0.108   6.970
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/library’
* installing *source* package ‘IdMappingAnalysis’ ...
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
** 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-.IdMapBase0.0850.0180.103
Bootstrap6.8140.1086.970
Corr0.4580.0140.489
CorrData0.0410.0040.045
CsvList.merge.Misc0.0020.0000.002
IdMap0.0060.0000.007
IdMapBase0.0020.0000.002
IdMapCounts0.3470.0170.368
IdMapDiff0.4790.0140.504
IdMapDiffCounts0.3590.0060.368
JointIdMap0.0760.0030.088
JointUniquePairs0.6230.0110.640
Mixture0.1770.0020.179
UniquePairs0.0030.0000.003
aligned.IdMapBase0.0060.0010.006
as.IdMap.UniquePairs0.0480.0010.050
as.MultiSet.CorrData0.4800.0150.500
as.UniquePairs.IdMap0.0250.0000.094
as.data.frame.IdMapBase0.0840.0010.086
as.data.frame.JointIdMap0.0520.0000.084
as.list.IdMap0.0100.0010.011
boxplot.JointUniquePairs0.0780.0020.295
byColNames.Subset0.0030.0000.004
byColumn.Subset0.0030.0010.004
byRow.Subset0.0050.0000.005
byRowNames.Subset0.0060.0000.007
clust.Mixture0.0020.0010.002
copy.Display000
corr.boxplot.JointUniquePairs0.0900.0030.126
corr.plot.JointUniquePairs0.0380.0020.054
create.Display000
create.UniquePairs0.1170.0020.120
diffCounts.plot.JointIdMap0.4980.0100.538
dim.IdMapBase0.0010.0000.001
dimnames.IdMapBase0.0010.0000.001
do.glm.JointUniquePairs0.0100.0000.011
ecdf.plot.JointIdMap0.2030.0030.210
equals.UniquePairs0.0450.0010.047
fisherTransform.DataFilter0.0010.0010.001
fisherTransformInverse.DataFilter000
fisherTransformJacobean.DataFilter000
getBootstrap.JointUniquePairs7.8510.1458.072
getCompoundEvents.IdMapDiffCounts0.3180.0060.328
getCompoundGroups.IdMapDiffCounts0.3100.0050.318
getCorr.JointUniquePairs0.0340.0010.035
getCorrData.JointUniquePairs0.0380.0010.039
getCorrDataFrame.JointUniquePairs0.0200.0010.020
getCounts.IdMap0.0130.0000.013
getCounts.JointIdMap0.1430.0060.150
getData.Corr0.0010.0010.001
getData.Mixture0.0010.0000.002
getDiff.JointIdMap0.1760.0060.182
getExperimentSet.CorrData0.0810.0030.084
getIdMapList.JointIdMap0.0760.0030.080
getMapNames.JointIdMap0.0550.0020.057
getMapNames.JointUniquePairs0.0010.0000.001
getMatch.UniquePairs0.0320.0020.034
getMatchInfo.JointIdMap0.0730.0040.079
getMatchInfo.JointUniquePairs0.2770.0030.279
getMixture.JointUniquePairs0.1310.0030.135
getSampleNames.CorrData0.0010.0000.002
getStats.IdMapCounts0.1700.0060.178
getStats.Mixture0.0030.0010.003
getUnionIdMap.JointIdMap0.4560.0100.472
getUniquePairs.Corr0.0020.0000.003
getUniquePairs.CorrData0.0040.0000.005
getUniquePairs.JointUniquePairs0.0040.0000.004
interactive.corr.boxplot.JointUniquePairs0.0510.0020.054
interactive.corr.plot.JointUniquePairs0.0290.0050.034
interactive.mixture.boxplot.JointUniquePairs0.1670.0100.179
interactive.mixture.plot.JointUniquePairs0.1280.0070.137
interactive.plot.CorrData0.0310.0010.032
interactive.plot.JointUniquePairs0.0000.0010.000
interleave.Misc000
line.loess.Display000
line.unsorted.Display000
logTen.DataFilter0.0630.0110.073
merge.IdMap0.5660.0070.575
minAvgCountConstraint.DataFilter0.0880.0060.095
minCountConstraint.DataFilter0.0930.0070.099
minCountGroupConstraint.DataFilter0.1090.0070.117
mixture.boxplot.JointUniquePairs0.1760.0040.182
mixture.plot.JointUniquePairs0.1440.0040.149
plot.Bootstrap0.0720.0020.075
plot.Corr0.0450.0030.049
plot.CorrData0.0220.0010.024
plot.IdMapCounts0.1850.0050.191
plot.IdMapDiffCounts0.5780.0130.597
plot.Mixture0.0120.0010.013
primaryIDs.IdMapBase0.0020.0010.002
primaryKey.CorrData0.0010.0000.001
primaryKey.IdMapBase0.0010.0000.001
primaryKey.Mixture0.0010.0010.000
progressMsg.Display000
removeNASeries.DataFilter0.0770.0070.084
secondaryKey.CorrData0.0010.0000.000
secondaryKey.IdMapBase0.0020.0000.001
secondaryKey.Mixture0.0000.0010.001
subsetCorr.JointUniquePairs0.0130.0000.013
subsetData.JointUniquePairs0.0180.0050.023
subsetGroups.JointUniquePairs0.5550.0080.566
summary.IdMapDiffCounts0.3550.0080.368
swapKeys.IdMap0.0510.0010.054
swapKeys.UniquePairs0.0220.0000.023
textBoundingBox.Display0.0000.0000.001
to.base.Misc0.0010.0000.001
to.binary.logical.Misc0.0010.0000.001
to.index.expr.Misc000
unique.UniquePairs0.0590.0020.062
words.Misc0.0000.0000.001
zoom.pars.Display000