BioC 3.5: CHECK report for IdMappingAnalysis on veracruz2

Package: IdMappingAnalysis

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz

StartedAt: 2017-10-18 04:56:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:57:38 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 76.6 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.20.0’
* 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... 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
getBootstrap.JointUniquePairs 5.501  0.052   5.703
Bootstrap                     5.462  0.058   5.639
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

* installing *source* package ‘IdMappingAnalysis’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IdMappingAnalysis)

name	user	system	elapsed
000-LB-.IdMapBase	0.234	0.014	0.253
Bootstrap	5.462	0.058	5.639
Corr	0.338	0.009	0.355
CorrData	0.119	0.002	0.123
CsvList.merge.Misc	0.002	0.000	0.003
IdMap	0.028	0.000	0.029
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.348	0.004	0.361
IdMapDiff	0.390	0.004	0.403
IdMapDiffCounts	0.356	0.003	0.368
JointIdMap	0.071	0.001	0.074
JointUniquePairs	0.650	0.006	0.668
Mixture	0.211	0.002	0.224
UniquePairs	0.003	0.001	0.003
aligned.IdMapBase	0.006	0.000	0.007
as.IdMap.UniquePairs	0.036	0.001	0.038
as.MultiSet.CorrData	0.500	0.007	0.532
as.UniquePairs.IdMap	0.019	0.000	0.020
as.data.frame.IdMapBase	0.202	0.001	0.208
as.data.frame.JointIdMap	0.053	0.000	0.055
as.list.IdMap	0.041	0.001	0.043
boxplot.JointUniquePairs	0.210	0.002	0.220
byColNames.Subset	0.004	0.000	0.005
byColumn.Subset	0.004	0.000	0.005
byRow.Subset	0.004	0.000	0.005
byRowNames.Subset	0.006	0.000	0.007
clust.Mixture	0.001	0.001	0.002
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.284	0.004	0.294
corr.plot.JointUniquePairs	0.042	0.002	0.044
create.Display	0.001	0.000	0.001
create.UniquePairs	0.114	0.002	0.121
diffCounts.plot.JointIdMap	0.484	0.004	0.498
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.001	0.002
do.glm.JointUniquePairs	0.014	0.000	0.014
ecdf.plot.JointIdMap	0.845	0.013	0.883
equals.UniquePairs	0.052	0.001	0.053
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.000
fisherTransformJacobean.DataFilter	0.000	0.000	0.001
getBootstrap.JointUniquePairs	5.501	0.052	5.703
getCompoundEvents.IdMapDiffCounts	0.357	0.003	0.370
getCompoundGroups.IdMapDiffCounts	0.445	0.003	0.460
getCorr.JointUniquePairs	0.135	0.003	0.145
getCorrData.JointUniquePairs	0.040	0.003	0.045
getCorrDataFrame.JointUniquePairs	0.019	0.001	0.020
getCounts.IdMap	0.014	0.001	0.015
getCounts.JointIdMap	0.146	0.003	0.159
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.001	0.001	0.002
getDiff.JointIdMap	0.192	0.003	0.204
getExperimentSet.CorrData	0.181	0.004	0.189
getIdMapList.JointIdMap	0.063	0.001	0.064
getMapNames.JointIdMap	0.057	0.003	0.060
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.040	0.001	0.041
getMatchInfo.JointIdMap	0.061	0.001	0.063
getMatchInfo.JointUniquePairs	0.300	0.002	0.309
getMixture.JointUniquePairs	0.125	0.001	0.131
getSampleNames.CorrData	0.003	0.000	0.002
getStats.IdMapCounts	0.227	0.003	0.235
getStats.Mixture	0.003	0.000	0.002
getUnionIdMap.JointIdMap	0.442	0.003	0.458
getUniquePairs.Corr	0.003	0.001	0.003
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.005	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.066	0.001	0.069
interactive.corr.plot.JointUniquePairs	0.094	0.006	0.102
interactive.mixture.boxplot.JointUniquePairs	0.169	0.005	0.180
interactive.mixture.plot.JointUniquePairs	0.206	0.006	0.217
interactive.plot.CorrData	0.035	0.001	0.038
interactive.plot.JointUniquePairs	0.001	0.001	0.001
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.000	0.000
line.unsorted.Display	0	0	0
logTen.DataFilter	0.081	0.004	0.089
merge.IdMap	0.615	0.004	0.635
minAvgCountConstraint.DataFilter	0.112	0.005	0.119
minCountConstraint.DataFilter	0.192	0.006	0.201
minCountGroupConstraint.DataFilter	0.137	0.006	0.144
mixture.boxplot.JointUniquePairs	0.167	0.002	0.173
mixture.plot.JointUniquePairs	0.121	0.001	0.127
plot.Bootstrap	0.109	0.002	0.117
plot.Corr	0.048	0.002	0.052
plot.CorrData	0.121	0.001	0.125
plot.IdMapCounts	0.237	0.002	0.242
plot.IdMapDiffCounts	0.718	0.004	0.738
plot.Mixture	0.016	0.000	0.016
primaryIDs.IdMapBase	0.003	0.001	0.004
primaryKey.CorrData	0.001	0.000	0.001
primaryKey.IdMapBase	0.003	0.000	0.002
primaryKey.Mixture	0.001	0.001	0.001
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.123	0.004	0.129
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.002	0.000	0.002
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.015	0.001	0.015
subsetData.JointUniquePairs	0.037	0.000	0.038
subsetGroups.JointUniquePairs	0.541	0.004	0.561
summary.IdMapDiffCounts	0.334	0.004	0.345
swapKeys.IdMap	0.072	0.001	0.074
swapKeys.UniquePairs	0.066	0.001	0.068
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.002	0.000	0.002
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.056	0.001	0.058
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0.001	0.000	0.001