BioC 3.6: CHECK report for IdMappingAnalysis on malbec1

Package: IdMappingAnalysis

Version: 1.21.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.21.0.tar.gz

StartedAt: 2017-08-16 00:00:40 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:01:44 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 63.8 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.21.0’
* 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 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-3.6-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	0.168	0.008	0.173
Bootstrap	4.148	0.004	4.155
Corr	0.244	0.000	0.247
CorrData	0.088	0.000	0.089
CsvList.merge.Misc	0.000	0.000	0.002
IdMap	0.016	0.000	0.019
IdMapBase	0.000	0.000	0.001
IdMapCounts	0.296	0.000	0.297
IdMapDiff	0.264	0.000	0.265
IdMapDiffCounts	0.200	0.004	0.202
JointIdMap	0.044	0.000	0.044
JointUniquePairs	0.516	0.000	0.516
Mixture	0.264	0.000	0.280
UniquePairs	0.004	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.004
as.IdMap.UniquePairs	0.032	0.000	0.031
as.MultiSet.CorrData	0.368	0.008	0.376
as.UniquePairs.IdMap	0.012	0.004	0.014
as.data.frame.IdMapBase	0.212	0.000	0.211
as.data.frame.JointIdMap	0.032	0.004	0.038
as.list.IdMap	0.028	0.000	0.029
boxplot.JointUniquePairs	0.100	0.000	0.101
byColNames.Subset	0.000	0.004	0.002
byColumn.Subset	0.004	0.000	0.003
byRow.Subset	0.004	0.000	0.003
byRowNames.Subset	0.004	0.000	0.004
clust.Mixture	0.000	0.000	0.002
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.212	0.000	0.214
corr.plot.JointUniquePairs	0.036	0.000	0.034
create.Display	0.000	0.000	0.001
create.UniquePairs	0.080	0.004	0.086
diffCounts.plot.JointIdMap	0.376	0.000	0.375
dim.IdMapBase	0.004	0.000	0.002
dimnames.IdMapBase	0.004	0.000	0.003
do.glm.JointUniquePairs	0.020	0.000	0.018
ecdf.plot.JointIdMap	0.696	0.008	0.704
equals.UniquePairs	0.064	0.000	0.063
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.000	0.001
getBootstrap.JointUniquePairs	4.272	0.000	4.275
getCompoundEvents.IdMapDiffCounts	0.200	0.000	0.201
getCompoundGroups.IdMapDiffCounts	0.212	0.000	0.211
getCorr.JointUniquePairs	0.096	0.000	0.098
getCorrData.JointUniquePairs	0.032	0.000	0.030
getCorrDataFrame.JointUniquePairs	0.016	0.000	0.018
getCounts.IdMap	0.012	0.000	0.012
getCounts.JointIdMap	0.104	0.000	0.105
getData.Corr	0	0	0
getData.Mixture	0.000	0.000	0.001
getDiff.JointIdMap	0.124	0.000	0.126
getExperimentSet.CorrData	0.120	0.004	0.126
getIdMapList.JointIdMap	0.060	0.000	0.058
getMapNames.JointIdMap	0.044	0.000	0.044
getMapNames.JointUniquePairs	0.004	0.000	0.001
getMatch.UniquePairs	0.032	0.000	0.031
getMatchInfo.JointIdMap	0.044	0.000	0.046
getMatchInfo.JointUniquePairs	0.224	0.000	0.224
getMixture.JointUniquePairs	0.144	0.000	0.146
getSampleNames.CorrData	0.000	0.000	0.001
getStats.IdMapCounts	0.164	0.000	0.163
getStats.Mixture	0.004	0.000	0.002
getUnionIdMap.JointIdMap	0.404	0.000	0.406
getUniquePairs.Corr	0.000	0.000	0.003
getUniquePairs.CorrData	0.004	0.000	0.003
getUniquePairs.JointUniquePairs	0.004	0.000	0.004
interactive.corr.boxplot.JointUniquePairs	0.048	0.000	0.049
interactive.corr.plot.JointUniquePairs	0.084	0.004	0.088
interactive.mixture.boxplot.JointUniquePairs	0.224	0.000	0.224
interactive.mixture.plot.JointUniquePairs	0.276	0.004	0.279
interactive.plot.CorrData	0.024	0.000	0.027
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	0.144	0.000	0.146
merge.IdMap	0.404	0.000	0.403
minAvgCountConstraint.DataFilter	0.084	0.000	0.084
minCountConstraint.DataFilter	0.088	0.000	0.087
minCountGroupConstraint.DataFilter	0.108	0.000	0.108
mixture.boxplot.JointUniquePairs	0.212	0.000	0.211
mixture.plot.JointUniquePairs	0.168	0.000	0.167
plot.Bootstrap	0.148	0.000	0.145
plot.Corr	0.056	0.008	0.064
plot.CorrData	0.144	0.000	0.141
plot.IdMapCounts	0.176	0.000	0.175
plot.IdMapDiffCounts	0.612	0.000	0.611
plot.Mixture	0.028	0.000	0.028
primaryIDs.IdMapBase	0.000	0.000	0.003
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.000	0.000	0.003
primaryKey.Mixture	0.000	0.000	0.002
progressMsg.Display	0.004	0.000	0.000
removeNASeries.DataFilter	0.144	0.008	0.153
secondaryKey.CorrData	0.000	0.000	0.002
secondaryKey.IdMapBase	0.004	0.000	0.003
secondaryKey.Mixture	0.004	0.000	0.001
subsetCorr.JointUniquePairs	0.016	0.000	0.017
subsetData.JointUniquePairs	0.040	0.004	0.042
subsetGroups.JointUniquePairs	0.420	0.004	0.422
summary.IdMapDiffCounts	0.284	0.000	0.284
swapKeys.IdMap	0.056	0.000	0.054
swapKeys.UniquePairs	0.048	0.000	0.047
textBoundingBox.Display	0	0	0
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.004	0.000	0.001
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.036	0.004	0.041
words.Misc	0.000	0.000	0.001
zoom.pars.Display	0	0	0