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CHECK report for IdMappingAnalysis on malbec2

This page was generated on 2018-10-17 08:24:12 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.24.0.tar.gz
StartedAt: 2018-10-16 01:13:59 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:14:56 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 57.1 seconds
RetCode: 0
Status:  OK 
CheckDir: IdMappingAnalysis.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.



Installation output

IdMappingAnalysis.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL IdMappingAnalysis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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-.IdMapBase0.0760.0040.082
Bootstrap4.8160.0124.825
Corr0.2600.0040.264
CorrData0.0240.0000.026
CsvList.merge.Misc0.0040.0000.002
IdMap0.0040.0000.004
IdMapBase0.0040.0000.001
IdMapCounts0.2000.0120.212
IdMapDiff0.2600.0080.267
IdMapDiffCounts0.2120.0040.214
JointIdMap0.0440.0000.044
JointUniquePairs0.3880.0000.386
Mixture0.2320.0000.230
UniquePairs0.0000.0000.002
aligned.IdMapBase0.0080.0000.005
as.IdMap.UniquePairs0.0240.0000.025
as.MultiSet.CorrData0.380.000.38
as.UniquePairs.IdMap0.0160.0000.015
as.data.frame.IdMapBase0.0600.0000.061
as.data.frame.JointIdMap0.0360.0000.039
as.list.IdMap0.0080.0000.007
boxplot.JointUniquePairs0.0480.0000.049
byColNames.Subset0.0040.0000.003
byColumn.Subset0.0040.0000.003
byRow.Subset0.0040.0000.003
byRowNames.Subset0.0040.0000.004
clust.Mixture0.0000.0000.002
copy.Display000
corr.boxplot.JointUniquePairs0.0600.0000.062
corr.plot.JointUniquePairs0.040.000.04
create.Display000
create.UniquePairs0.0840.0000.085
diffCounts.plot.JointIdMap0.3760.0000.378
dim.IdMapBase0.0040.0000.001
dimnames.IdMapBase0.0000.0000.002
do.glm.JointUniquePairs0.0080.0000.010
ecdf.plot.JointIdMap0.1640.0000.164
equals.UniquePairs0.0240.0000.028
fisherTransform.DataFilter000
fisherTransformInverse.DataFilter0.0000.0000.001
fisherTransformJacobean.DataFilter0.0000.0000.001
getBootstrap.JointUniquePairs4.9280.0124.939
getCompoundEvents.IdMapDiffCounts0.1960.0000.194
getCompoundGroups.IdMapDiffCounts0.20.00.2
getCorr.JointUniquePairs0.0360.0000.035
getCorrData.JointUniquePairs0.0280.0000.029
getCorrDataFrame.JointUniquePairs0.0160.0000.013
getCounts.IdMap0.0200.0000.021
getCounts.JointIdMap0.0920.0040.094
getData.Corr0.0000.0000.001
getData.Mixture0.0000.0000.001
getDiff.JointIdMap0.1200.0040.123
getExperimentSet.CorrData0.0480.0080.056
getIdMapList.JointIdMap0.0480.0000.045
getMapNames.JointIdMap0.0440.0040.048
getMapNames.JointUniquePairs0.0000.0000.001
getMatch.UniquePairs0.0280.0000.030
getMatchInfo.JointIdMap0.040.000.04
getMatchInfo.JointUniquePairs0.2320.0000.233
getMixture.JointUniquePairs0.1440.0000.144
getSampleNames.CorrData0.0040.0000.002
getStats.IdMapCounts0.1000.0040.105
getStats.Mixture0.0040.0000.002
getUnionIdMap.JointIdMap0.2920.0000.290
getUniquePairs.Corr0.0040.0000.003
getUniquePairs.CorrData0.0000.0000.003
getUniquePairs.JointUniquePairs0.0000.0000.003
interactive.corr.boxplot.JointUniquePairs0.0480.0000.048
interactive.corr.plot.JointUniquePairs0.0320.0000.030
interactive.mixture.boxplot.JointUniquePairs0.1560.0000.159
interactive.mixture.plot.JointUniquePairs0.1440.0040.148
interactive.plot.CorrData0.0280.0000.027
interactive.plot.JointUniquePairs000
interleave.Misc0.0040.0000.002
line.loess.Display0.0000.0000.001
line.unsorted.Display000
logTen.DataFilter0.0520.0000.051
merge.IdMap0.4320.0040.437
minAvgCountConstraint.DataFilter0.0640.0000.068
minCountConstraint.DataFilter0.0760.0000.079
minCountGroupConstraint.DataFilter0.0920.0000.092
mixture.boxplot.JointUniquePairs0.1720.0000.174
mixture.plot.JointUniquePairs0.1440.0000.145
plot.Bootstrap0.0680.0000.068
plot.Corr0.0360.0000.037
plot.CorrData0.0160.0000.016
plot.IdMapCounts0.1200.0000.118
plot.IdMapDiffCounts0.3640.0040.366
plot.Mixture0.0200.0000.019
primaryIDs.IdMapBase0.0000.0000.002
primaryKey.CorrData0.0040.0000.000
primaryKey.IdMapBase0.0000.0000.003
primaryKey.Mixture0.0000.0000.001
progressMsg.Display0.0000.0000.001
removeNASeries.DataFilter0.0920.0000.088
secondaryKey.CorrData0.0000.0000.002
secondaryKey.IdMapBase0.0000.0000.001
secondaryKey.Mixture0.0000.0000.001
subsetCorr.JointUniquePairs0.0120.0000.009
subsetData.JointUniquePairs0.0080.0000.007
subsetGroups.JointUniquePairs0.4640.0000.465
summary.IdMapDiffCounts0.2040.0000.204
swapKeys.IdMap0.0400.0000.038
swapKeys.UniquePairs0.0160.0000.015
textBoundingBox.Display000
to.base.Misc0.0040.0000.001
to.binary.logical.Misc0.0080.0000.008
to.index.expr.Misc0.0000.0000.001
unique.UniquePairs0.0440.0000.041
words.Misc0.0000.0000.001
zoom.pars.Display0.0040.0000.002