BioC 3.4: CHECK report for IdMappingAnalysis on malbec1

Package: IdMappingAnalysis

Version: 1.18.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.18.0.tar.gz

StartedAt: 2017-04-14 23:16:37 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:17:33 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 56.2 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.18.0’
* 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-3.4-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	0.192	0.000	0.194
Bootstrap	3.680	0.008	3.688
Corr	0.216	0.000	0.216
CorrData	0.032	0.000	0.032
CsvList.merge.Misc	0.000	0.000	0.002
IdMap	0.008	0.000	0.005
IdMapBase	0.000	0.000	0.001
IdMapCounts	0.284	0.000	0.284
IdMapDiff	0.280	0.000	0.282
IdMapDiffCounts	0.204	0.004	0.208
JointIdMap	0.048	0.000	0.045
JointUniquePairs	0.424	0.008	0.434
Mixture	0.232	0.000	0.233
UniquePairs	0.000	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.005
as.IdMap.UniquePairs	0.036	0.000	0.035
as.MultiSet.CorrData	0.416	0.000	0.415
as.UniquePairs.IdMap	0.016	0.000	0.015
as.data.frame.IdMapBase	0.040	0.000	0.039
as.data.frame.JointIdMap	0.040	0.000	0.043
as.list.IdMap	0.008	0.000	0.010
boxplot.JointUniquePairs	0.044	0.000	0.044
byColNames.Subset	0.004	0.000	0.003
byColumn.Subset	0.004	0.000	0.002
byRow.Subset	0.004	0.000	0.003
byRowNames.Subset	0.004	0.000	0.005
clust.Mixture	0.000	0.000	0.001
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.060	0.000	0.059
corr.plot.JointUniquePairs	0.032	0.008	0.038
create.Display	0	0	0
create.UniquePairs	0.096	0.000	0.096
diffCounts.plot.JointIdMap	0.336	0.004	0.336
dim.IdMapBase	0.000	0.000	0.002
dimnames.IdMapBase	0.004	0.000	0.002
do.glm.JointUniquePairs	0.012	0.000	0.011
ecdf.plot.JointIdMap	0.164	0.000	0.165
equals.UniquePairs	0.028	0.004	0.029
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	4.288	0.000	4.294
getCompoundEvents.IdMapDiffCounts	0.252	0.000	0.252
getCompoundGroups.IdMapDiffCounts	0.228	0.000	0.229
getCorr.JointUniquePairs	0.036	0.000	0.037
getCorrData.JointUniquePairs	0.036	0.000	0.035
getCorrDataFrame.JointUniquePairs	0.016	0.000	0.013
getCounts.IdMap	0.016	0.000	0.017
getCounts.JointIdMap	0.184	0.004	0.186
getData.Corr	0.004	0.000	0.001
getData.Mixture	0.000	0.004	0.002
getDiff.JointIdMap	0.232	0.000	0.233
getExperimentSet.CorrData	0.052	0.008	0.059
getIdMapList.JointIdMap	0.048	0.000	0.046
getMapNames.JointIdMap	0.040	0.000	0.041
getMapNames.JointUniquePairs	0.000	0.000	0.002
getMatch.UniquePairs	0.032	0.000	0.031
getMatchInfo.JointIdMap	0.044	0.000	0.042
getMatchInfo.JointUniquePairs	0.24	0.00	0.24
getMixture.JointUniquePairs	0.228	0.000	0.226
getSampleNames.CorrData	0.004	0.000	0.003
getStats.IdMapCounts	0.152	0.004	0.155
getStats.Mixture	0.004	0.000	0.003
getUnionIdMap.JointIdMap	0.380	0.004	0.383
getUniquePairs.Corr	0.004	0.000	0.004
getUniquePairs.CorrData	0.008	0.000	0.005
getUniquePairs.JointUniquePairs	0.004	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.064	0.000	0.063
interactive.corr.plot.JointUniquePairs	0.048	0.000	0.048
interactive.mixture.boxplot.JointUniquePairs	0.328	0.000	0.324
interactive.mixture.plot.JointUniquePairs	0.248	0.004	0.253
interactive.plot.CorrData	0.044	0.000	0.046
interactive.plot.JointUniquePairs	0.000	0.000	0.001
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.000	0.000	0.001
line.unsorted.Display	0.000	0.000	0.001
logTen.DataFilter	0.088	0.000	0.088
merge.IdMap	0.568	0.000	0.566
minAvgCountConstraint.DataFilter	0.096	0.000	0.095
minCountConstraint.DataFilter	0.12	0.00	0.12
minCountGroupConstraint.DataFilter	0.144	0.000	0.144
mixture.boxplot.JointUniquePairs	0.236	0.000	0.235
mixture.plot.JointUniquePairs	0.180	0.000	0.179
plot.Bootstrap	0.080	0.004	0.083
plot.Corr	0.064	0.004	0.068
plot.CorrData	0.024	0.000	0.021
plot.IdMapCounts	0.200	0.000	0.202
plot.IdMapDiffCounts	0.512	0.004	0.517
plot.Mixture	0.024	0.000	0.024
primaryIDs.IdMapBase	0.004	0.000	0.002
primaryKey.CorrData	0.004	0.000	0.002
primaryKey.IdMapBase	0.000	0.000	0.003
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.132	0.008	0.138
secondaryKey.CorrData	0.004	0.000	0.002
secondaryKey.IdMapBase	0.004	0.000	0.003
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.020	0.000	0.017
subsetData.JointUniquePairs	0.008	0.000	0.009
subsetGroups.JointUniquePairs	0.568	0.000	0.571
summary.IdMapDiffCounts	0.336	0.000	0.336
swapKeys.IdMap	0.060	0.000	0.062
swapKeys.UniquePairs	0.020	0.000	0.023
textBoundingBox.Display	0	0	0
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.000	0.000	0.002
to.index.expr.Misc	0.004	0.000	0.002
unique.UniquePairs	0.076	0.000	0.074
words.Misc	0.000	0.000	0.001
zoom.pars.Display	0	0	0