BioC 3.3: CHECK report for IdMappingAnalysis on oaxaca

Package: IdMappingAnalysis

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.16.0.tar.gz

StartedAt: 2016-10-13 02:49:36 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:50:57 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 81.6 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_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.16.0’
* 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 5.966  0.055   6.029
Bootstrap                     5.864  0.061   5.963
* 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-3.3-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	0.188	0.012	0.200
Bootstrap	5.864	0.061	5.963
Corr	0.345	0.008	0.353
CorrData	0.043	0.001	0.044
CsvList.merge.Misc	0.003	0.001	0.002
IdMap	0.005	0.000	0.005
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.423	0.009	0.433
IdMapDiff	0.447	0.003	0.450
IdMapDiffCounts	0.371	0.002	0.373
JointIdMap	0.073	0.001	0.074
JointUniquePairs	0.651	0.003	0.655
Mixture	0.191	0.001	0.226
UniquePairs	0.003	0.000	0.003
aligned.IdMapBase	0.008	0.000	0.008
as.IdMap.UniquePairs	0.039	0.001	0.041
as.MultiSet.CorrData	0.583	0.008	0.595
as.UniquePairs.IdMap	0.022	0.001	0.023
as.data.frame.IdMapBase	0.063	0.001	0.064
as.data.frame.JointIdMap	0.063	0.001	0.064
as.list.IdMap	0.014	0.000	0.014
boxplot.JointUniquePairs	0.062	0.002	0.065
byColNames.Subset	0.005	0.000	0.005
byColumn.Subset	0.005	0.001	0.005
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.007	0.001	0.008
clust.Mixture	0.002	0.000	0.002
copy.Display	0.000	0.001	0.000
corr.boxplot.JointUniquePairs	0.074	0.002	0.076
corr.plot.JointUniquePairs	0.048	0.003	0.051
create.Display	0	0	0
create.UniquePairs	0.115	0.001	0.117
diffCounts.plot.JointIdMap	0.474	0.002	0.476
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.001	0.002
do.glm.JointUniquePairs	0.015	0.000	0.015
ecdf.plot.JointIdMap	0.189	0.007	0.197
equals.UniquePairs	0.043	0.000	0.044
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.000	0.001
getBootstrap.JointUniquePairs	5.966	0.055	6.029
getCompoundEvents.IdMapDiffCounts	0.351	0.002	0.352
getCompoundGroups.IdMapDiffCounts	0.373	0.007	0.380
getCorr.JointUniquePairs	0.044	0.001	0.053
getCorrData.JointUniquePairs	0.058	0.004	0.062
getCorrDataFrame.JointUniquePairs	0.017	0.001	0.018
getCounts.IdMap	0.026	0.000	0.026
getCounts.JointIdMap	0.137	0.003	0.139
getData.Corr	0.000	0.001	0.001
getData.Mixture	0.001	0.000	0.001
getDiff.JointIdMap	0.262	0.010	0.272
getExperimentSet.CorrData	0.062	0.003	0.066
getIdMapList.JointIdMap	0.069	0.002	0.071
getMapNames.JointIdMap	0.05	0.00	0.05
getMapNames.JointUniquePairs	0.001	0.001	0.002
getMatch.UniquePairs	0.031	0.000	0.031
getMatchInfo.JointIdMap	0.071	0.003	0.074
getMatchInfo.JointUniquePairs	0.319	0.001	0.320
getMixture.JointUniquePairs	0.138	0.002	0.140
getSampleNames.CorrData	0.003	0.001	0.003
getStats.IdMapCounts	0.175	0.004	0.179
getStats.Mixture	0.004	0.000	0.004
getUnionIdMap.JointIdMap	0.435	0.003	0.437
getUniquePairs.Corr	0.005	0.001	0.005
getUniquePairs.CorrData	0.005	0.000	0.005
getUniquePairs.JointUniquePairs	0.003	0.000	0.003
interactive.corr.boxplot.JointUniquePairs	0.078	0.001	0.079
interactive.corr.plot.JointUniquePairs	0.045	0.006	0.051
interactive.mixture.boxplot.JointUniquePairs	0.182	0.006	0.187
interactive.mixture.plot.JointUniquePairs	0.147	0.005	0.152
interactive.plot.CorrData	0.044	0.001	0.046
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.000	0.000
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.001	0.001
logTen.DataFilter	0.154	0.008	0.163
merge.IdMap	0.607	0.005	0.613
minAvgCountConstraint.DataFilter	0.100	0.004	0.104
minCountConstraint.DataFilter	0.111	0.004	0.116
minCountGroupConstraint.DataFilter	0.162	0.007	0.170
mixture.boxplot.JointUniquePairs	0.166	0.001	0.174
mixture.plot.JointUniquePairs	0.133	0.001	0.135
plot.Bootstrap	0.080	0.001	0.092
plot.Corr	0.054	0.002	0.058
plot.CorrData	0.029	0.001	0.029
plot.IdMapCounts	0.189	0.001	0.197
plot.IdMapDiffCounts	0.615	0.005	0.621
plot.Mixture	0.023	0.001	0.025
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.004	0.001	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.132	0.003	0.135
secondaryKey.CorrData	0.001	0.001	0.001
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.014	0.001	0.014
subsetData.JointUniquePairs	0.020	0.004	0.025
subsetGroups.JointUniquePairs	0.615	0.003	0.617
summary.IdMapDiffCounts	0.404	0.002	0.406
swapKeys.IdMap	0.056	0.000	0.057
swapKeys.UniquePairs	0.023	0.000	0.023
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.001	0.000	0.002
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.139	0.003	0.142
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.000	0.000	0.001