Package: IdMappingAnalysis

Version: 1.27.0

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_1.27.0.tar.gz

StartedAt: 2019-04-09 01:19:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:20:48 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 67.5 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running 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_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IdMappingAnalysis.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.27.0’
* 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
* 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	0.110	0.016	0.126
Bootstrap	4.470	0.023	4.506
Corr	0.320	0.010	0.331
CorrData	0.036	0.001	0.037
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.006	0.000	0.006
IdMapBase	0.001	0.000	0.001
IdMapCounts	0.327	0.008	0.337
IdMapDiff	0.353	0.004	0.361
IdMapDiffCounts	0.219	0.000	0.219
JointIdMap	0.046	0.000	0.045
JointUniquePairs	0.423	0.004	0.427
Mixture	0.226	0.000	0.241
UniquePairs	0.001	0.000	0.001
aligned.IdMapBase	0.003	0.000	0.003
as.IdMap.UniquePairs	0.028	0.000	0.028
as.MultiSet.CorrData	0.391	0.002	0.392
as.UniquePairs.IdMap	0.014	0.000	0.015
as.data.frame.IdMapBase	0.063	0.000	0.063
as.data.frame.JointIdMap	0.032	0.004	0.036
as.list.IdMap	0.006	0.000	0.006
boxplot.JointUniquePairs	0.043	0.003	0.047
byColNames.Subset	0.002	0.000	0.003
byColumn.Subset	0.002	0.000	0.002
byRow.Subset	0.002	0.000	0.002
byRowNames.Subset	0.003	0.000	0.003
clust.Mixture	0.001	0.000	0.001
copy.Display	0.001	0.000	0.000
corr.boxplot.JointUniquePairs	0.061	0.000	0.060
corr.plot.JointUniquePairs	0.032	0.000	0.031
create.Display	0.001	0.000	0.000
create.UniquePairs	0.08	0.00	0.08
diffCounts.plot.JointIdMap	0.495	0.000	0.495
dim.IdMapBase	0.001	0.000	0.001
dimnames.IdMapBase	0.001	0.000	0.001
do.glm.JointUniquePairs	0.016	0.000	0.016
ecdf.plot.JointIdMap	0.215	0.004	0.219
equals.UniquePairs	0.040	0.003	0.043
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.000	0.001
getBootstrap.JointUniquePairs	4.360	0.016	4.372
getCompoundEvents.IdMapDiffCounts	0.191	0.000	0.190
getCompoundGroups.IdMapDiffCounts	0.192	0.000	0.191
getCorr.JointUniquePairs	0.032	0.000	0.033
getCorrData.JointUniquePairs	0.033	0.000	0.034
getCorrDataFrame.JointUniquePairs	0.012	0.000	0.012
getCounts.IdMap	0.011	0.000	0.011
getCounts.JointIdMap	0.180	0.000	0.181
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.000	0.002
getDiff.JointIdMap	0.148	0.004	0.152
getExperimentSet.CorrData	0.052	0.004	0.056
getIdMapList.JointIdMap	0.042	0.000	0.042
getMapNames.JointIdMap	0.045	0.000	0.045
getMapNames.JointUniquePairs	0.001	0.000	0.001
getMatch.UniquePairs	0.028	0.000	0.028
getMatchInfo.JointIdMap	0.039	0.000	0.039
getMatchInfo.JointUniquePairs	0.352	0.000	0.352
getMixture.JointUniquePairs	0.145	0.000	0.144
getSampleNames.CorrData	0.001	0.000	0.001
getStats.IdMapCounts	0.100	0.003	0.102
getStats.Mixture	0.002	0.000	0.002
getUnionIdMap.JointIdMap	0.316	0.000	0.316
getUniquePairs.Corr	0.002	0.000	0.003
getUniquePairs.CorrData	0.003	0.000	0.003
getUniquePairs.JointUniquePairs	0.002	0.001	0.002
interactive.corr.boxplot.JointUniquePairs	0.046	0.002	0.048
interactive.corr.plot.JointUniquePairs	0.026	0.004	0.030
interactive.mixture.boxplot.JointUniquePairs	0.163	0.000	0.162
interactive.mixture.plot.JointUniquePairs	0.152	0.000	0.151
interactive.plot.CorrData	0.026	0.000	0.027
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	0.037	0.004	0.041
merge.IdMap	0.699	0.004	0.703
minAvgCountConstraint.DataFilter	0.092	0.000	0.092
minCountConstraint.DataFilter	0.115	0.000	0.115
minCountGroupConstraint.DataFilter	0.138	0.000	0.138
mixture.boxplot.JointUniquePairs	0.266	0.000	0.265
mixture.plot.JointUniquePairs	0.218	0.004	0.223
plot.Bootstrap	0.098	0.000	0.099
plot.Corr	0.041	0.000	0.040
plot.CorrData	0.026	0.004	0.030
plot.IdMapCounts	0.167	0.000	0.168
plot.IdMapDiffCounts	0.402	0.000	0.402
plot.Mixture	0.022	0.000	0.022
primaryIDs.IdMapBase	0.002	0.000	0.002
primaryKey.CorrData	0	0	0
primaryKey.IdMapBase	0.002	0.000	0.002
primaryKey.Mixture	0.001	0.000	0.000
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.085	0.004	0.089
secondaryKey.CorrData	0	0	0
secondaryKey.IdMapBase	0.001	0.000	0.001
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.006	0.004	0.010
subsetData.JointUniquePairs	0.007	0.000	0.007
subsetGroups.JointUniquePairs	0.402	0.000	0.401
summary.IdMapDiffCounts	0.192	0.004	0.195
swapKeys.IdMap	0.042	0.000	0.042
swapKeys.UniquePairs	0.013	0.000	0.013
textBoundingBox.Display	0.001	0.000	0.000
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.000	0.000	0.001
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.040	0.000	0.039
words.Misc	0.001	0.000	0.000
zoom.pars.Display	0	0	0