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CHECK report for IdMappingAnalysis on merida1

This page was generated on 2019-04-16 11:56:16 -0400 (Tue, 16 Apr 2019).

Package 759/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.26.0
Alex Lisovich , Roger Day
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: RELEASE_3_8
Last Commit: 3e4929f
Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: IdMappingAnalysis
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2019-04-16 00:39:33 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:40:46 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 72.3 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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.26.0’
* 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
Bootstrap                     7.673  0.101   7.879
getBootstrap.JointUniquePairs 7.214  0.071   7.327
* 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-3.8-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-.IdMapBase0.0850.0170.102
Bootstrap7.6730.1017.879
Corr0.4290.0130.443
CorrData0.0410.0020.043
CsvList.merge.Misc0.0010.0000.002
IdMap0.0030.0000.004
IdMapBase0.0010.0000.001
IdMapCounts0.3270.0100.338
IdMapDiff0.4490.0100.462
IdMapDiffCounts0.4040.0080.413
JointIdMap0.0650.0020.067
JointUniquePairs0.6150.0090.632
Mixture0.2080.0020.213
UniquePairs0.0020.0010.003
aligned.IdMapBase0.0050.0000.005
as.IdMap.UniquePairs0.0440.0010.045
as.MultiSet.CorrData0.4830.0110.497
as.UniquePairs.IdMap0.0150.0000.016
as.data.frame.IdMapBase0.1110.0020.112
as.data.frame.JointIdMap0.0670.0020.069
as.list.IdMap0.0110.0000.012
boxplot.JointUniquePairs0.0600.0020.062
byColNames.Subset0.0030.0000.004
byColumn.Subset0.0130.0000.016
byRow.Subset0.0030.0000.003
byRowNames.Subset0.0040.0000.004
clust.Mixture0.0010.0000.001
copy.Display000
corr.boxplot.JointUniquePairs0.0930.0010.094
corr.plot.JointUniquePairs0.0500.0010.053
create.Display0.0010.0000.001
create.UniquePairs0.1330.0020.139
diffCounts.plot.JointIdMap0.5080.0020.511
dim.IdMapBase0.0010.0000.001
dimnames.IdMapBase0.0010.0000.001
do.glm.JointUniquePairs0.0110.0000.011
ecdf.plot.JointIdMap0.2020.0010.204
equals.UniquePairs0.0380.0000.039
fisherTransform.DataFilter0.0010.0000.000
fisherTransformInverse.DataFilter0.0000.0010.000
fisherTransformJacobean.DataFilter000
getBootstrap.JointUniquePairs7.2140.0717.327
getCompoundEvents.IdMapDiffCounts0.3130.0050.319
getCompoundGroups.IdMapDiffCounts0.3760.0040.383
getCorr.JointUniquePairs0.0480.0010.050
getCorrData.JointUniquePairs0.0450.0010.048
getCorrDataFrame.JointUniquePairs0.0170.0000.020
getCounts.IdMap0.0190.0000.019
getCounts.JointIdMap0.1460.0030.151
getData.Corr000
getData.Mixture0.0010.0000.001
getDiff.JointIdMap0.2290.0050.235
getExperimentSet.CorrData0.0920.0050.098
getIdMapList.JointIdMap0.0800.0030.082
getMapNames.JointIdMap0.0740.0040.080
getMapNames.JointUniquePairs0.0010.0000.002
getMatch.UniquePairs0.0360.0010.036
getMatchInfo.JointIdMap0.0690.0000.068
getMatchInfo.JointUniquePairs0.3660.0010.367
getMixture.JointUniquePairs0.1480.0010.150
getSampleNames.CorrData0.0010.0000.001
getStats.IdMapCounts0.1610.0030.166
getStats.Mixture0.0030.0000.004
getUnionIdMap.JointIdMap0.4610.0030.470
getUniquePairs.Corr0.0030.0010.004
getUniquePairs.CorrData0.0030.0000.004
getUniquePairs.JointUniquePairs0.0020.0000.003
interactive.corr.boxplot.JointUniquePairs0.0690.0010.071
interactive.corr.plot.JointUniquePairs0.0400.0050.045
interactive.mixture.boxplot.JointUniquePairs0.1980.0060.206
interactive.mixture.plot.JointUniquePairs0.1330.0060.139
interactive.plot.CorrData0.0320.0010.033
interactive.plot.JointUniquePairs0.0000.0000.001
interleave.Misc000
line.loess.Display000
line.unsorted.Display000
logTen.DataFilter0.1020.0090.111
merge.IdMap0.6070.0020.612
minAvgCountConstraint.DataFilter0.0860.0040.091
minCountConstraint.DataFilter0.1020.0110.113
minCountGroupConstraint.DataFilter0.1230.0080.132
mixture.boxplot.JointUniquePairs0.1710.0020.173
mixture.plot.JointUniquePairs0.1210.0020.123
plot.Bootstrap0.0700.0020.071
plot.Corr0.0480.0020.051
plot.CorrData0.0260.0000.027
plot.IdMapCounts0.1750.0010.178
plot.IdMapDiffCounts0.5940.0040.602
plot.Mixture0.0160.0010.017
primaryIDs.IdMapBase0.0020.0000.001
primaryKey.CorrData0.0000.0000.001
primaryKey.IdMapBase0.0010.0000.002
primaryKey.Mixture0.0010.0000.001
progressMsg.Display0.0010.0000.000
removeNASeries.DataFilter0.1310.0040.137
secondaryKey.CorrData0.0010.0000.001
secondaryKey.IdMapBase0.0010.0010.001
secondaryKey.Mixture0.0010.0000.000
subsetCorr.JointUniquePairs0.010.000.01
subsetData.JointUniquePairs0.0130.0010.014
subsetGroups.JointUniquePairs0.6080.0070.617
summary.IdMapDiffCounts0.3860.0040.392
swapKeys.IdMap0.0410.0010.041
swapKeys.UniquePairs0.0150.0000.016
textBoundingBox.Display000
to.base.Misc0.0010.0000.000
to.binary.logical.Misc0.0010.0000.001
to.index.expr.Misc0.0000.0000.001
unique.UniquePairs0.0420.0010.043
words.Misc0.0010.0000.000
zoom.pars.Display000