Package: IdMappingAnalysis

Version: 1.30.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.30.0.tar.gz

StartedAt: 2020-04-15 01:15:36 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:16:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 62.7 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:IdMappingAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings IdMappingAnalysis_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.30.0’
* 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 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 5.172  0.016   5.187
* 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-3.10-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL IdMappingAnalysis
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

name	user	system	elapsed
000-LB-.IdMapBase	0.112	0.020	0.131
Bootstrap	5.172	0.016	5.187
Corr	0.228	0.004	0.231
CorrData	0.04	0.00	0.04
CsvList.merge.Misc	0.000	0.000	0.002
IdMap	0.008	0.000	0.006
IdMapBase	0.000	0.000	0.001
IdMapCounts	0.312	0.004	0.315
IdMapDiff	0.356	0.004	0.360
IdMapDiffCounts	0.344	0.000	0.345
JointIdMap	0.068	0.000	0.068
JointUniquePairs	0.536	0.004	0.540
Mixture	0.344	0.000	0.347
UniquePairs	0.004	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.005
as.IdMap.UniquePairs	0.044	0.000	0.043
as.MultiSet.CorrData	0.644	0.000	0.642
as.UniquePairs.IdMap	0.024	0.000	0.022
as.data.frame.IdMapBase	0.088	0.000	0.094
as.data.frame.JointIdMap	0.056	0.000	0.056
as.list.IdMap	0.008	0.000	0.009
boxplot.JointUniquePairs	0.060	0.000	0.058
byColNames.Subset	0.004	0.000	0.003
byColumn.Subset	0.004	0.000	0.003
byRow.Subset	0.004	0.000	0.002
byRowNames.Subset	0.004	0.000	0.004
clust.Mixture	0.004	0.000	0.001
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.076	0.004	0.081
corr.plot.JointUniquePairs	0.044	0.000	0.043
create.Display	0	0	0
create.UniquePairs	0.096	0.000	0.096
diffCounts.plot.JointIdMap	0.484	0.004	0.487
dim.IdMapBase	0.000	0.000	0.001
dimnames.IdMapBase	0.000	0.000	0.002
do.glm.JointUniquePairs	0.020	0.000	0.018
ecdf.plot.JointIdMap	0.176	0.000	0.177
equals.UniquePairs	0.024	0.000	0.026
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	4.184	0.024	4.210
getCompoundEvents.IdMapDiffCounts	0.264	0.012	0.276
getCompoundGroups.IdMapDiffCounts	0.372	0.004	0.377
getCorr.JointUniquePairs	0.048	0.000	0.046
getCorrData.JointUniquePairs	0.028	0.000	0.031
getCorrDataFrame.JointUniquePairs	0.012	0.000	0.015
getCounts.IdMap	0.016	0.000	0.015
getCounts.JointIdMap	0.188	0.008	0.196
getData.Corr	0	0	0
getData.Mixture	0.000	0.000	0.002
getDiff.JointIdMap	0.188	0.000	0.189
getExperimentSet.CorrData	0.072	0.000	0.076
getIdMapList.JointIdMap	0.048	0.000	0.050
getMapNames.JointIdMap	0.072	0.004	0.075
getMapNames.JointUniquePairs	0.000	0.000	0.001
getMatch.UniquePairs	0.064	0.000	0.066
getMatchInfo.JointIdMap	0.072	0.000	0.069
getMatchInfo.JointUniquePairs	0.428	0.000	0.427
getMixture.JointUniquePairs	0.236	0.000	0.238
getSampleNames.CorrData	0.000	0.000	0.002
getStats.IdMapCounts	0.18	0.00	0.18
getStats.Mixture	0.004	0.000	0.003
getUnionIdMap.JointIdMap	0.600	0.008	0.609
getUniquePairs.Corr	0.004	0.000	0.005
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.004	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.080	0.000	0.078
interactive.corr.plot.JointUniquePairs	0.032	0.000	0.032
interactive.mixture.boxplot.JointUniquePairs	0.276	0.000	0.276
interactive.mixture.plot.JointUniquePairs	0.148	0.000	0.147
interactive.plot.CorrData	0.024	0.000	0.026
interactive.plot.JointUniquePairs	0.000	0.000	0.001
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
logTen.DataFilter	0.048	0.000	0.048
merge.IdMap	0.532	0.000	0.534
minAvgCountConstraint.DataFilter	0.104	0.000	0.107
minCountConstraint.DataFilter	0.108	0.004	0.112
minCountGroupConstraint.DataFilter	0.116	0.000	0.117
mixture.boxplot.JointUniquePairs	0.192	0.000	0.190
mixture.plot.JointUniquePairs	0.188	0.000	0.186
plot.Bootstrap	0.096	0.000	0.096
plot.Corr	0.056	0.000	0.060
plot.CorrData	0.024	0.000	0.028
plot.IdMapCounts	0.188	0.000	0.189
plot.IdMapDiffCounts	0.612	0.000	0.610
plot.Mixture	0.028	0.000	0.028
primaryIDs.IdMapBase	0.004	0.000	0.003
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.004	0.000	0.002
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.164	0.004	0.168
secondaryKey.CorrData	0.000	0.000	0.001
secondaryKey.IdMapBase	0.000	0.000	0.002
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.016	0.000	0.014
subsetData.JointUniquePairs	0.008	0.000	0.008
subsetGroups.JointUniquePairs	0.716	0.004	0.722
summary.IdMapDiffCounts	0.368	0.000	0.367
swapKeys.IdMap	0.064	0.000	0.064
swapKeys.UniquePairs	0.020	0.004	0.025
textBoundingBox.Display	0	0	0
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.004	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.072	0.000	0.072
words.Misc	0.000	0.000	0.001
zoom.pars.Display	0	0	0