BioC 3.6: CHECK report for IdMappingAnalysis on veracruz1

Package: IdMappingAnalysis

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.21.0.tar.gz

StartedAt: 2017-08-16 04:26:34 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:27:48 -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_1.21.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.21.0’
* 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 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
Bootstrap                     5.207  0.061   5.442
getBootstrap.JointUniquePairs 5.172  0.044   5.359
* 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-3.6-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	0.201	0.012	0.225
Bootstrap	5.207	0.061	5.442
Corr	0.348	0.011	0.359
CorrData	0.119	0.003	0.121
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.028	0.001	0.030
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.341	0.006	0.353
IdMapDiff	0.406	0.006	0.421
IdMapDiffCounts	0.362	0.002	0.376
JointIdMap	0.123	0.001	0.132
JointUniquePairs	0.537	0.007	0.561
Mixture	0.208	0.002	0.212
UniquePairs	0.003	0.001	0.003
aligned.IdMapBase	0.007	0.000	0.007
as.IdMap.UniquePairs	0.037	0.000	0.043
as.MultiSet.CorrData	0.432	0.003	0.441
as.UniquePairs.IdMap	0.022	0.000	0.030
as.data.frame.IdMapBase	0.230	0.002	0.253
as.data.frame.JointIdMap	0.048	0.003	0.052
as.list.IdMap	0.037	0.001	0.038
boxplot.JointUniquePairs	0.126	0.001	0.131
byColNames.Subset	0.004	0.000	0.005
byColumn.Subset	0.003	0.000	0.003
byRow.Subset	0.005	0.000	0.004
byRowNames.Subset	0.006	0.000	0.007
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.291	0.002	0.299
corr.plot.JointUniquePairs	0.043	0.002	0.048
create.Display	0	0	0
create.UniquePairs	0.118	0.000	0.118
diffCounts.plot.JointIdMap	0.444	0.002	0.465
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.000	0.002
do.glm.JointUniquePairs	0.014	0.001	0.014
ecdf.plot.JointIdMap	0.844	0.007	0.891
equals.UniquePairs	0.044	0.000	0.046
fisherTransform.DataFilter	0.001	0.000	0.000
fisherTransformInverse.DataFilter	0.001	0.000	0.000
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	5.172	0.044	5.359
getCompoundEvents.IdMapDiffCounts	0.278	0.004	0.287
getCompoundGroups.IdMapDiffCounts	0.390	0.005	0.404
getCorr.JointUniquePairs	0.115	0.001	0.121
getCorrData.JointUniquePairs	0.037	0.002	0.038
getCorrDataFrame.JointUniquePairs	0.015	0.000	0.015
getCounts.IdMap	0.015	0.000	0.016
getCounts.JointIdMap	0.135	0.002	0.145
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.002	0.000	0.002
getDiff.JointIdMap	0.164	0.002	0.168
getExperimentSet.CorrData	0.179	0.004	0.183
getIdMapList.JointIdMap	0.064	0.001	0.066
getMapNames.JointIdMap	0.057	0.001	0.059
getMapNames.JointUniquePairs	0.003	0.001	0.006
getMatch.UniquePairs	0.042	0.000	0.043
getMatchInfo.JointIdMap	0.055	0.001	0.056
getMatchInfo.JointUniquePairs	0.288	0.000	0.291
getMixture.JointUniquePairs	0.117	0.001	0.123
getSampleNames.CorrData	0.003	0.000	0.002
getStats.IdMapCounts	0.196	0.003	0.203
getStats.Mixture	0.003	0.000	0.003
getUnionIdMap.JointIdMap	0.446	0.009	0.469
getUniquePairs.Corr	0.003	0.000	0.003
getUniquePairs.CorrData	0.003	0.000	0.003
getUniquePairs.JointUniquePairs	0.004	0.000	0.004
interactive.corr.boxplot.JointUniquePairs	0.061	0.001	0.066
interactive.corr.plot.JointUniquePairs	0.098	0.005	0.106
interactive.mixture.boxplot.JointUniquePairs	0.173	0.005	0.187
interactive.mixture.plot.JointUniquePairs	0.213	0.006	0.222
interactive.plot.CorrData	0.034	0.001	0.036
interactive.plot.JointUniquePairs	0.001	0.001	0.001
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.080	0.005	0.089
merge.IdMap	0.606	0.008	0.621
minAvgCountConstraint.DataFilter	0.108	0.005	0.122
minCountConstraint.DataFilter	0.105	0.005	0.115
minCountGroupConstraint.DataFilter	0.132	0.008	0.142
mixture.boxplot.JointUniquePairs	0.163	0.001	0.167
mixture.plot.JointUniquePairs	0.120	0.001	0.123
plot.Bootstrap	0.104	0.001	0.113
plot.Corr	0.040	0.001	0.041
plot.CorrData	0.119	0.001	0.121
plot.IdMapCounts	0.254	0.003	0.260
plot.IdMapDiffCounts	0.698	0.005	0.734
plot.Mixture	0.016	0.001	0.020
primaryIDs.IdMapBase	0.002	0.001	0.003
primaryKey.CorrData	0.001	0.000	0.002
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.104	0.003	0.108
secondaryKey.CorrData	0.001	0.000	0.002
secondaryKey.IdMapBase	0.002	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.014	0.000	0.014
subsetData.JointUniquePairs	0.031	0.000	0.032
subsetGroups.JointUniquePairs	0.555	0.001	0.571
summary.IdMapDiffCounts	0.319	0.002	0.332
swapKeys.IdMap	0.076	0.001	0.081
swapKeys.UniquePairs	0.065	0.000	0.071
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	0.001	0.001	0.001
unique.UniquePairs	0.053	0.000	0.056
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.001	0.000	0.001