BioC 3.5: CHECK report for IdMappingAnalysis on malbec2

Package: IdMappingAnalysis

Version: 1.20.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz

StartedAt: 2017-08-15 23:53:46 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:54:48 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 61.9 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘1.20.0’
* 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 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-3.5-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	0.208	0.008	0.213
Bootstrap	4.268	0.004	4.275
Corr	0.248	0.004	0.251
CorrData	0.088	0.000	0.087
CsvList.merge.Misc	0.004	0.000	0.002
IdMap	0.016	0.000	0.017
IdMapBase	0.000	0.000	0.001
IdMapCounts	0.308	0.000	0.309
IdMapDiff	0.272	0.000	0.270
IdMapDiffCounts	0.208	0.000	0.209
JointIdMap	0.044	0.000	0.044
JointUniquePairs	0.528	0.004	0.534
Mixture	0.252	0.000	0.270
UniquePairs	0.000	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.004
as.IdMap.UniquePairs	0.028	0.000	0.030
as.MultiSet.CorrData	0.380	0.000	0.377
as.UniquePairs.IdMap	0.012	0.004	0.015
as.data.frame.IdMapBase	0.208	0.000	0.210
as.data.frame.JointIdMap	0.044	0.000	0.043
as.list.IdMap	0.032	0.000	0.030
boxplot.JointUniquePairs	0.104	0.000	0.104
byColNames.Subset	0.004	0.000	0.003
byColumn.Subset	0.004	0.000	0.003
byRow.Subset	0.000	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	0.220	0.000	0.221
corr.plot.JointUniquePairs	0.036	0.000	0.034
create.Display	0.000	0.000	0.001
create.UniquePairs	0.132	0.000	0.132
diffCounts.plot.JointIdMap	0.564	0.000	0.563
dim.IdMapBase	0.004	0.000	0.002
dimnames.IdMapBase	0.004	0.000	0.003
do.glm.JointUniquePairs	0.020	0.000	0.019
ecdf.plot.JointIdMap	1.044	0.000	1.046
equals.UniquePairs	0.04	0.00	0.04
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	4.24	0.00	4.24
getCompoundEvents.IdMapDiffCounts	0.200	0.004	0.203
getCompoundGroups.IdMapDiffCounts	0.204	0.004	0.208
getCorr.JointUniquePairs	0.1	0.0	0.1
getCorrData.JointUniquePairs	0.028	0.000	0.030
getCorrDataFrame.JointUniquePairs	0.020	0.000	0.018
getCounts.IdMap	0.012	0.000	0.012
getCounts.JointIdMap	0.108	0.000	0.106
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.004	0.000	0.001
getDiff.JointIdMap	0.124	0.000	0.125
getExperimentSet.CorrData	0.128	0.004	0.128
getIdMapList.JointIdMap	0.060	0.000	0.059
getMapNames.JointIdMap	0.044	0.000	0.043
getMapNames.JointUniquePairs	0.000	0.000	0.001
getMatch.UniquePairs	0.032	0.000	0.030
getMatchInfo.JointIdMap	0.048	0.000	0.047
getMatchInfo.JointUniquePairs	0.256	0.000	0.257
getMixture.JointUniquePairs	0.144	0.000	0.146
getSampleNames.CorrData	0.004	0.000	0.001
getStats.IdMapCounts	0.164	0.000	0.166
getStats.Mixture	0.000	0.000	0.002
getUnionIdMap.JointIdMap	0.336	0.000	0.333
getUniquePairs.Corr	0.004	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	0.004	0.051
interactive.corr.plot.JointUniquePairs	0.088	0.000	0.086
interactive.mixture.boxplot.JointUniquePairs	0.176	0.000	0.177
interactive.mixture.plot.JointUniquePairs	0.232	0.000	0.232
interactive.plot.CorrData	0.028	0.000	0.027
interactive.plot.JointUniquePairs	0.004	0.000	0.000
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0.004	0.000	0.000
logTen.DataFilter	0.160	0.000	0.159
merge.IdMap	0.400	0.008	0.408
minAvgCountConstraint.DataFilter	0.092	0.000	0.092
minCountConstraint.DataFilter	0.092	0.004	0.094
minCountGroupConstraint.DataFilter	0.116	0.004	0.119
mixture.boxplot.JointUniquePairs	0.192	0.000	0.193
mixture.plot.JointUniquePairs	0.188	0.000	0.191
plot.Bootstrap	0.096	0.000	0.095
plot.Corr	0.044	0.000	0.040
plot.CorrData	0.084	0.000	0.084
plot.IdMapCounts	0.168	0.000	0.169
plot.IdMapDiffCounts	0.472	0.000	0.469
plot.Mixture	0.016	0.000	0.017
primaryIDs.IdMapBase	0.000	0.000	0.002
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.000	0.000	0.001
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.084	0.000	0.086
secondaryKey.CorrData	0.000	0.000	0.001
secondaryKey.IdMapBase	0.004	0.000	0.001
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.012	0.000	0.010
subsetData.JointUniquePairs	0.028	0.000	0.027
subsetGroups.JointUniquePairs	0.408	0.000	0.411
summary.IdMapDiffCounts	0.208	0.000	0.210
swapKeys.IdMap	0.052	0.000	0.055
swapKeys.UniquePairs	0.048	0.000	0.047
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.000	0.000	0.001
to.index.expr.Misc	0.004	0.000	0.000
unique.UniquePairs	0.040	0.000	0.039
words.Misc	0.000	0.000	0.001
zoom.pars.Display	0	0	0