Package: IdMappingAnalysis

Version: 1.28.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.28.0.tar.gz

StartedAt: 2019-10-16 02:27:58 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:29:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 66.5 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.28.0’
* 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 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 5.632  0.039   5.667
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IdMappingAnalysis
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
000-LB-.IdMapBase	0.095	0.028	0.122
Bootstrap	5.632	0.039	5.667
Corr	0.354	0.000	0.354
CorrData	0.039	0.000	0.039
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.002	0.004	0.005
IdMapBase	0.001	0.000	0.001
IdMapCounts	0.357	0.004	0.361
IdMapDiff	0.386	0.012	0.398
IdMapDiffCounts	0.221	0.000	0.221
JointIdMap	0.039	0.002	0.042
JointUniquePairs	0.414	0.001	0.415
Mixture	0.230	0.000	0.244
UniquePairs	0.002	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.003
as.IdMap.UniquePairs	0.024	0.000	0.024
as.MultiSet.CorrData	0.369	0.004	0.373
as.UniquePairs.IdMap	0.020	0.000	0.019
as.data.frame.IdMapBase	0.070	0.000	0.069
as.data.frame.JointIdMap	0.057	0.000	0.057
as.list.IdMap	0.011	0.000	0.011
boxplot.JointUniquePairs	0.057	0.000	0.057
byColNames.Subset	0.003	0.000	0.004
byColumn.Subset	0.004	0.000	0.004
byRow.Subset	0.004	0.000	0.004
byRowNames.Subset	0.005	0.000	0.005
clust.Mixture	0.001	0.000	0.001
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.062	0.004	0.067
corr.plot.JointUniquePairs	0.032	0.000	0.032
create.Display	0	0	0
create.UniquePairs	0.115	0.000	0.115
diffCounts.plot.JointIdMap	0.540	0.004	0.543
dim.IdMapBase	0.001	0.000	0.001
dimnames.IdMapBase	0.001	0.000	0.001
do.glm.JointUniquePairs	0.015	0.000	0.016
ecdf.plot.JointIdMap	0.234	0.000	0.233
equals.UniquePairs	0.045	0.000	0.044
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	4.002	0.008	4.007
getCompoundEvents.IdMapDiffCounts	0.197	0.004	0.201
getCompoundGroups.IdMapDiffCounts	0.203	0.000	0.202
getCorr.JointUniquePairs	0.032	0.000	0.032
getCorrData.JointUniquePairs	0.025	0.000	0.026
getCorrDataFrame.JointUniquePairs	0.019	0.000	0.019
getCounts.IdMap	0.011	0.000	0.011
getCounts.JointIdMap	0.088	0.000	0.089
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.000	0.000	0.001
getDiff.JointIdMap	0.144	0.004	0.148
getExperimentSet.CorrData	0.096	0.004	0.100
getIdMapList.JointIdMap	0.071	0.000	0.070
getMapNames.JointIdMap	0.079	0.000	0.079
getMapNames.JointUniquePairs	0.001	0.000	0.002
getMatch.UniquePairs	0.055	0.000	0.054
getMatchInfo.JointIdMap	0.066	0.000	0.066
getMatchInfo.JointUniquePairs	0.401	0.000	0.401
getMixture.JointUniquePairs	0.235	0.000	0.235
getSampleNames.CorrData	0.001	0.000	0.001
getStats.IdMapCounts	0.185	0.000	0.185
getStats.Mixture	0.003	0.000	0.003
getUnionIdMap.JointIdMap	0.614	0.000	0.613
getUniquePairs.Corr	0.004	0.000	0.004
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.002	0.001	0.004
interactive.corr.boxplot.JointUniquePairs	0.073	0.002	0.075
interactive.corr.plot.JointUniquePairs	0.042	0.004	0.045
interactive.mixture.boxplot.JointUniquePairs	0.282	0.000	0.281
interactive.mixture.plot.JointUniquePairs	0.226	0.004	0.230
interactive.plot.CorrData	0.038	0.000	0.038
interactive.plot.JointUniquePairs	0	0	0
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
logTen.DataFilter	0.081	0.001	0.082
merge.IdMap	0.678	0.004	0.682
minAvgCountConstraint.DataFilter	0.104	0.000	0.104
minCountConstraint.DataFilter	0.107	0.008	0.114
minCountGroupConstraint.DataFilter	0.137	0.000	0.137
mixture.boxplot.JointUniquePairs	0.277	0.000	0.277
mixture.plot.JointUniquePairs	0.227	0.000	0.227
plot.Bootstrap	0.085	0.000	0.084
plot.Corr	0.035	0.000	0.035
plot.CorrData	0.016	0.000	0.015
plot.IdMapCounts	0.111	0.000	0.111
plot.IdMapDiffCounts	0.411	0.004	0.414
plot.Mixture	0.017	0.000	0.017
primaryIDs.IdMapBase	0.001	0.000	0.002
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.001	0.000	0.001
primaryKey.Mixture	0.001	0.000	0.000
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.103	0.004	0.106
secondaryKey.CorrData	0.000	0.000	0.001
secondaryKey.IdMapBase	0.001	0.000	0.001
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.011	0.000	0.010
subsetData.JointUniquePairs	0.006	0.000	0.006
subsetGroups.JointUniquePairs	0.451	0.004	0.455
summary.IdMapDiffCounts	0.184	0.004	0.188
swapKeys.IdMap	0.034	0.000	0.034
swapKeys.UniquePairs	0.013	0.000	0.014
textBoundingBox.Display	0	0	0
to.base.Misc	0	0	0
to.binary.logical.Misc	0.000	0.000	0.001
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.041	0.000	0.040
words.Misc	0	0	0
zoom.pars.Display	0	0	0