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CHECK report for IdMappingAnalysis on merida1

This page was generated on 2020-04-15 12:37:37 -0400 (Wed, 15 Apr 2020).

Package 826/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.30.0
Alex Lisovich , Roger Day
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: RELEASE_3_10
Last Commit: 09eecf9
Last Changed Date: 2019-10-29 13:08:28 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  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: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2020-04-15 03:07:58 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:09:10 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 71.6 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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.30.0’
* 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
* 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-3.10-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
** 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-.IdMapBase0.0670.0130.081
Bootstrap4.0370.1014.152
Corr0.3160.0150.334
CorrData0.0290.0020.031
CsvList.merge.Misc0.0010.0000.001
IdMap0.0030.0000.004
IdMapBase0.0010.0000.001
IdMapCounts0.2590.0120.271
IdMapDiff0.3250.0090.337
IdMapDiffCounts0.3070.0040.312
JointIdMap0.0530.0040.057
JointUniquePairs0.4980.0060.504
Mixture0.1640.0010.166
UniquePairs0.0020.0000.002
aligned.IdMapBase0.0030.0000.004
as.IdMap.UniquePairs0.0290.0010.030
as.MultiSet.CorrData0.4060.0100.415
as.UniquePairs.IdMap0.0290.0000.030
as.data.frame.IdMapBase0.0810.0010.083
as.data.frame.JointIdMap0.0500.0010.051
as.list.IdMap0.0120.0010.013
boxplot.JointUniquePairs0.0610.0020.063
byColNames.Subset0.0050.0000.005
byColumn.Subset0.0050.0000.006
byRow.Subset0.0050.0000.005
byRowNames.Subset0.0040.0000.004
clust.Mixture0.0010.0010.001
copy.Display0.0010.0000.000
corr.boxplot.JointUniquePairs0.0840.0010.088
corr.plot.JointUniquePairs0.0420.0020.044
create.Display000
create.UniquePairs0.1330.0020.136
diffCounts.plot.JointIdMap0.4250.0030.429
dim.IdMapBase0.0010.0000.001
dimnames.IdMapBase0.0010.0000.001
do.glm.JointUniquePairs0.0100.0000.011
ecdf.plot.JointIdMap0.1680.0030.172
equals.UniquePairs0.0340.0000.035
fisherTransform.DataFilter000
fisherTransformInverse.DataFilter000
fisherTransformJacobean.DataFilter0.0010.0000.000
getBootstrap.JointUniquePairs4.2940.0754.394
getCompoundEvents.IdMapDiffCounts0.3340.0080.349
getCompoundGroups.IdMapDiffCounts0.3620.0030.367
getCorr.JointUniquePairs0.0410.0010.043
getCorrData.JointUniquePairs0.0410.0010.042
getCorrDataFrame.JointUniquePairs0.0190.0000.019
getCounts.IdMap0.0210.0010.021
getCounts.JointIdMap0.1490.0030.153
getData.Corr0.0010.0010.000
getData.Mixture0.0010.0000.001
getDiff.JointIdMap0.1870.0020.191
getExperimentSet.CorrData0.0920.0030.095
getIdMapList.JointIdMap0.0760.0010.080
getMapNames.JointIdMap0.0510.0010.052
getMapNames.JointUniquePairs0.0010.0000.001
getMatch.UniquePairs0.0390.0020.042
getMatchInfo.JointIdMap0.0480.0010.048
getMatchInfo.JointUniquePairs0.3580.0030.365
getMixture.JointUniquePairs0.1130.0010.116
getSampleNames.CorrData0.0020.0010.003
getStats.IdMapCounts0.1220.0060.128
getStats.Mixture0.0020.0000.002
getUnionIdMap.JointIdMap0.4910.0070.497
getUniquePairs.Corr0.0030.0000.003
getUniquePairs.CorrData0.0030.0000.004
getUniquePairs.JointUniquePairs0.0030.0000.003
interactive.corr.boxplot.JointUniquePairs0.0520.0020.054
interactive.corr.plot.JointUniquePairs0.0390.0070.047
interactive.mixture.boxplot.JointUniquePairs0.1660.0090.176
interactive.mixture.plot.JointUniquePairs0.1360.0070.144
interactive.plot.CorrData0.0390.0010.041
interactive.plot.JointUniquePairs0.0000.0010.001
interleave.Misc000
line.loess.Display0.0000.0000.001
line.unsorted.Display0.0010.0000.001
logTen.DataFilter0.0580.0040.065
merge.IdMap0.6080.0030.616
minAvgCountConstraint.DataFilter0.1000.0050.106
minCountConstraint.DataFilter0.1250.0100.135
minCountGroupConstraint.DataFilter0.1360.0070.144
mixture.boxplot.JointUniquePairs0.1670.0020.170
mixture.plot.JointUniquePairs0.1320.0020.135
plot.Bootstrap0.0750.0020.078
plot.Corr0.0470.0020.049
plot.CorrData0.0260.0010.029
plot.IdMapCounts0.1480.0020.153
plot.IdMapDiffCounts0.5280.0040.541
plot.Mixture0.0170.0010.018
primaryIDs.IdMapBase0.0020.0010.002
primaryKey.CorrData0.0010.0000.001
primaryKey.IdMapBase0.0010.0000.002
primaryKey.Mixture000
progressMsg.Display000
removeNASeries.DataFilter0.1180.0090.129
secondaryKey.CorrData0.0060.0000.007
secondaryKey.IdMapBase0.0020.0000.003
secondaryKey.Mixture000
subsetCorr.JointUniquePairs0.0130.0000.014
subsetData.JointUniquePairs0.0090.0010.010
subsetGroups.JointUniquePairs0.5600.0050.573
summary.IdMapDiffCounts0.3800.0050.387
swapKeys.IdMap0.0500.0010.051
swapKeys.UniquePairs0.0250.0010.026
textBoundingBox.Display0.0010.0000.000
to.base.Misc0.0000.0000.001
to.binary.logical.Misc0.0020.0000.002
to.index.expr.Misc0.0000.0000.001
unique.UniquePairs0.0690.0010.070
words.Misc0.0010.0000.001
zoom.pars.Display0.0010.0000.001