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: 2017-08-16 04:11:08 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:12:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 74.3 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 3.4.1 (2017-06-30)
* 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 5.275  0.046   5.490
Bootstrap                     5.082  0.064   5.317
* 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	0.215	0.012	0.232
Bootstrap	5.082	0.064	5.317
Corr	0.332	0.010	0.352
CorrData	0.128	0.003	0.132
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.027	0.000	0.026
IdMapBase	0.002	0.000	0.001
IdMapCounts	0.314	0.004	0.325
IdMapDiff	0.358	0.004	0.379
IdMapDiffCounts	0.313	0.004	0.318
JointIdMap	0.118	0.004	0.124
JointUniquePairs	0.582	0.004	0.611
Mixture	0.213	0.000	0.221
UniquePairs	0.003	0.000	0.003
aligned.IdMapBase	0.006	0.000	0.006
as.IdMap.UniquePairs	0.034	0.001	0.035
as.MultiSet.CorrData	0.444	0.006	0.458
as.UniquePairs.IdMap	0.021	0.000	0.022
as.data.frame.IdMapBase	0.253	0.001	0.256
as.data.frame.JointIdMap	0.052	0.001	0.060
as.list.IdMap	0.044	0.000	0.044
boxplot.JointUniquePairs	0.123	0.002	0.125
byColNames.Subset	0.005	0.000	0.005
byColumn.Subset	0.004	0.001	0.004
byRow.Subset	0.005	0.000	0.004
byRowNames.Subset	0.006	0.001	0.006
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.261	0.002	0.269
corr.plot.JointUniquePairs	0.039	0.001	0.041
create.Display	0.000	0.000	0.001
create.UniquePairs	0.118	0.000	0.119
diffCounts.plot.JointIdMap	0.466	0.002	0.486
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.001	0.000	0.002
do.glm.JointUniquePairs	0.015	0.001	0.015
ecdf.plot.JointIdMap	0.877	0.017	0.918
equals.UniquePairs	0.050	0.001	0.052
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.001	0.001
getBootstrap.JointUniquePairs	5.275	0.046	5.490
getCompoundEvents.IdMapDiffCounts	0.296	0.004	0.308
getCompoundGroups.IdMapDiffCounts	0.421	0.003	0.443
getCorr.JointUniquePairs	0.128	0.002	0.132
getCorrData.JointUniquePairs	0.039	0.002	0.045
getCorrDataFrame.JointUniquePairs	0.013	0.001	0.014
getCounts.IdMap	0.018	0.000	0.018
getCounts.JointIdMap	0.119	0.003	0.126
getData.Corr	0.001	0.000	0.000
getData.Mixture	0.001	0.000	0.002
getDiff.JointIdMap	0.153	0.003	0.164
getExperimentSet.CorrData	0.174	0.003	0.183
getIdMapList.JointIdMap	0.061	0.000	0.062
getMapNames.JointIdMap	0.053	0.000	0.053
getMapNames.JointUniquePairs	0.002	0.000	0.003
getMatch.UniquePairs	0.049	0.001	0.050
getMatchInfo.JointIdMap	0.053	0.001	0.055
getMatchInfo.JointUniquePairs	0.285	0.001	0.292
getMixture.JointUniquePairs	0.115	0.001	0.120
getSampleNames.CorrData	0.003	0.001	0.002
getStats.IdMapCounts	0.211	0.002	0.215
getStats.Mixture	0.002	0.000	0.003
getUnionIdMap.JointIdMap	0.445	0.008	0.454
getUniquePairs.Corr	0.004	0.000	0.005
getUniquePairs.CorrData	0.005	0.001	0.006
getUniquePairs.JointUniquePairs	0.005	0.000	0.009
interactive.corr.boxplot.JointUniquePairs	0.058	0.001	0.059
interactive.corr.plot.JointUniquePairs	0.108	0.004	0.116
interactive.mixture.boxplot.JointUniquePairs	0.156	0.005	0.167
interactive.mixture.plot.JointUniquePairs	0.197	0.006	0.210
interactive.plot.CorrData	0.026	0.001	0.026
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.001	0.001
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
logTen.DataFilter	0.075	0.004	0.079
merge.IdMap	0.659	0.009	0.682
minAvgCountConstraint.DataFilter	0.095	0.003	0.100
minCountConstraint.DataFilter	0.098	0.003	0.101
minCountGroupConstraint.DataFilter	0.135	0.009	0.144
mixture.boxplot.JointUniquePairs	0.149	0.001	0.157
mixture.plot.JointUniquePairs	0.132	0.002	0.136
plot.Bootstrap	0.099	0.002	0.102
plot.Corr	0.047	0.001	0.049
plot.CorrData	0.108	0.001	0.114
plot.IdMapCounts	0.234	0.001	0.246
plot.IdMapDiffCounts	0.710	0.004	0.729
plot.Mixture	0.014	0.001	0.015
primaryIDs.IdMapBase	0.002	0.000	0.002
primaryKey.CorrData	0.001	0.001	0.001
primaryKey.IdMapBase	0.002	0.000	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.102	0.004	0.111
secondaryKey.CorrData	0.001	0.000	0.001
secondaryKey.IdMapBase	0.003	0.000	0.002
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.013	0.001	0.020
subsetData.JointUniquePairs	0.034	0.000	0.034
subsetGroups.JointUniquePairs	0.566	0.002	0.588
summary.IdMapDiffCounts	0.312	0.001	0.327
swapKeys.IdMap	0.057	0.001	0.058
swapKeys.UniquePairs	0.063	0.000	0.066
textBoundingBox.Display	0.001	0.000	0.000
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.045	0.000	0.046
words.Misc	0.002	0.000	0.002
zoom.pars.Display	0.000	0.000	0.001