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CHECK report for IdMappingAnalysis on celaya2

This page was generated on 2019-10-16 12:49:56 -0400 (Wed, 16 Oct 2019).

Package 796/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.28.0
Alex Lisovich , Roger Day
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: RELEASE_3_9
Last Commit: b112768
Last Changed Date: 2019-05-02 11:53:35 -0400 (Thu, 02 May 2019)
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

Summary

Package: IdMappingAnalysis
Version: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2019-10-16 03:46:26 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:48:07 -0400 (Wed, 16 Oct 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_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.28.0’
* 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 : : 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 : : 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 6.099  0.218   6.310
Bootstrap                     6.026  0.267   6.285
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IdMappingAnalysis)

Tests output


Example timings

IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings

nameusersystemelapsed
000-LB-.IdMapBase0.1190.0360.155
Bootstrap6.0260.2676.285
Corr0.4300.0430.473
CorrData0.0580.0100.068
CsvList.merge.Misc0.0030.0000.003
IdMap0.0080.0010.009
IdMapBase0.0020.0000.002
IdMapCounts0.4170.0360.454
IdMapDiff0.5630.0180.580
IdMapDiffCounts0.4620.0190.480
JointIdMap0.0660.0060.072
JointUniquePairs0.6550.0140.668
Mixture0.2290.0060.236
UniquePairs0.0030.0000.003
aligned.IdMapBase0.0070.0010.008
as.IdMap.UniquePairs0.0530.0040.056
as.MultiSet.CorrData0.6490.0210.670
as.UniquePairs.IdMap0.0170.0010.018
as.data.frame.IdMapBase0.0890.0010.090
as.data.frame.JointIdMap0.0480.0010.050
as.list.IdMap0.0080.0000.009
boxplot.JointUniquePairs0.0470.0020.049
byColNames.Subset0.0040.0000.004
byColumn.Subset0.0130.0030.014
byRow.Subset0.0030.0000.003
byRowNames.Subset0.0040.0000.005
clust.Mixture0.0010.0010.001
copy.Display0.0010.0000.001
corr.boxplot.JointUniquePairs0.0770.0020.078
corr.plot.JointUniquePairs0.0530.0030.057
create.Display0.0000.0010.000
create.UniquePairs0.1600.0020.163
diffCounts.plot.JointIdMap0.7160.0120.729
dim.IdMapBase0.0020.0000.003
dimnames.IdMapBase0.0010.0000.001
do.glm.JointUniquePairs0.0180.0010.018
ecdf.plot.JointIdMap0.2460.0100.256
equals.UniquePairs0.0380.0000.039
fisherTransform.DataFilter0.0010.0000.000
fisherTransformInverse.DataFilter0.0000.0010.000
fisherTransformJacobean.DataFilter0.0010.0010.001
getBootstrap.JointUniquePairs6.0990.2186.310
getCompoundEvents.IdMapDiffCounts0.2790.0170.296
getCompoundGroups.IdMapDiffCounts0.3560.0080.363
getCorr.JointUniquePairs0.0680.0030.070
getCorrData.JointUniquePairs0.0600.0110.071
getCorrDataFrame.JointUniquePairs0.0140.0010.016
getCounts.IdMap0.0150.0000.016
getCounts.JointIdMap0.1780.0080.186
getData.Corr0.0000.0010.001
getData.Mixture0.0020.0010.003
getDiff.JointIdMap0.1770.0180.194
getExperimentSet.CorrData0.1180.0090.126
getIdMapList.JointIdMap0.0900.0090.099
getMapNames.JointIdMap0.1020.0110.113
getMapNames.JointUniquePairs0.0010.0010.002
getMatch.UniquePairs0.0340.0010.035
getMatchInfo.JointIdMap0.0590.0020.060
getMatchInfo.JointUniquePairs0.5560.0080.563
getMixture.JointUniquePairs0.1280.0020.131
getSampleNames.CorrData0.0030.0010.005
getStats.IdMapCounts0.1860.0080.194
getStats.Mixture0.0020.0000.003
getUnionIdMap.JointIdMap0.5840.0240.606
getUniquePairs.Corr0.0030.0000.003
getUniquePairs.CorrData0.0030.0000.004
getUniquePairs.JointUniquePairs0.0030.0000.004
interactive.corr.boxplot.JointUniquePairs0.0500.0020.052
interactive.corr.plot.JointUniquePairs0.0330.0090.041
interactive.mixture.boxplot.JointUniquePairs0.1490.0110.159
interactive.mixture.plot.JointUniquePairs0.1220.0090.131
interactive.plot.CorrData0.0320.0010.034
interactive.plot.JointUniquePairs0.0010.0000.000
interleave.Misc0.0010.0000.001
line.loess.Display0.0010.0000.000
line.unsorted.Display000
logTen.DataFilter0.0560.0110.067
merge.IdMap0.8480.0150.862
minAvgCountConstraint.DataFilter0.0730.0060.078
minCountConstraint.DataFilter0.1200.0210.140
minCountGroupConstraint.DataFilter0.2030.0180.220
mixture.boxplot.JointUniquePairs0.2170.0040.221
mixture.plot.JointUniquePairs0.1630.0070.169
plot.Bootstrap0.0850.0030.089
plot.Corr0.0720.0100.081
plot.CorrData0.0310.0010.034
plot.IdMapCounts0.1530.0090.162
plot.IdMapDiffCounts0.7390.0150.752
plot.Mixture0.0150.0010.016
primaryIDs.IdMapBase0.0020.0010.002
primaryKey.CorrData0.0010.0000.001
primaryKey.IdMapBase0.0020.0000.002
primaryKey.Mixture0.0010.0000.001
progressMsg.Display0.0000.0000.001
removeNASeries.DataFilter0.1210.0150.135
secondaryKey.CorrData0.0020.0000.002
secondaryKey.IdMapBase0.0030.0000.003
secondaryKey.Mixture0.0000.0000.001
subsetCorr.JointUniquePairs0.0170.0010.018
subsetData.JointUniquePairs0.0110.0000.011
subsetGroups.JointUniquePairs0.6810.0120.693
summary.IdMapDiffCounts0.5120.0140.525
swapKeys.IdMap0.0690.0020.071
swapKeys.UniquePairs0.0300.0020.032
textBoundingBox.Display0.0000.0010.000
to.base.Misc0.0020.0000.001
to.binary.logical.Misc0.0020.0000.002
to.index.expr.Misc000
unique.UniquePairs0.0790.0040.083
words.Misc0.0010.0000.001
zoom.pars.Display0.0000.0010.000