BioC 3.5: CHECK report for IdMappingAnalysis on oaxaca

Package: IdMappingAnalysis

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.19.0.tar.gz

StartedAt: 2017-03-04 04:29:02 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:30:27 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 85.2 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_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IdMappingAnalysis.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.19.0’
* 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                     6.131  0.084   6.218
getBootstrap.JointUniquePairs 5.956  0.072   6.064
* 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	0.225	0.014	0.238
Bootstrap	6.131	0.084	6.218
Corr	0.331	0.011	0.342
CorrData	0.100	0.004	0.104
CsvList.merge.Misc	0.001	0.000	0.001
IdMap	0.027	0.000	0.028
IdMapBase	0.002	0.001	0.002
IdMapCounts	0.351	0.011	0.362
IdMapDiff	0.369	0.001	0.370
IdMapDiffCounts	0.384	0.003	0.387
JointIdMap	0.054	0.002	0.057
JointUniquePairs	0.533	0.006	0.538
Mixture	0.226	0.001	0.266
UniquePairs	0.002	0.000	0.002
aligned.IdMapBase	0.007	0.001	0.007
as.IdMap.UniquePairs	0.052	0.000	0.052
as.MultiSet.CorrData	0.615	0.014	0.629
as.UniquePairs.IdMap	0.025	0.001	0.025
as.data.frame.IdMapBase	0.244	0.002	0.246
as.data.frame.JointIdMap	0.065	0.002	0.067
as.list.IdMap	0.048	0.001	0.048
boxplot.JointUniquePairs	0.155	0.002	0.156
byColNames.Subset	0.005	0.000	0.005
byColumn.Subset	0.004	0.001	0.004
byRow.Subset	0.003	0.000	0.003
byRowNames.Subset	0.004	0.000	0.005
clust.Mixture	0.002	0.001	0.002
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.285	0.002	0.287
corr.plot.JointUniquePairs	0.044	0.002	0.046
create.Display	0.000	0.001	0.001
create.UniquePairs	0.114	0.000	0.115
diffCounts.plot.JointIdMap	0.602	0.005	0.607
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.000	0.001
do.glm.JointUniquePairs	0.014	0.001	0.015
ecdf.plot.JointIdMap	0.977	0.011	0.988
equals.UniquePairs	0.043	0.000	0.043
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.001	0.001
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	5.956	0.072	6.064
getCompoundEvents.IdMapDiffCounts	0.359	0.004	0.363
getCompoundGroups.IdMapDiffCounts	0.412	0.007	0.420
getCorr.JointUniquePairs	0.140	0.002	0.141
getCorrData.JointUniquePairs	0.052	0.001	0.053
getCorrDataFrame.JointUniquePairs	0.020	0.001	0.020
getCounts.IdMap	0.017	0.000	0.017
getCounts.JointIdMap	0.096	0.000	0.096
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.001	0.000	0.001
getDiff.JointIdMap	0.169	0.002	0.171
getExperimentSet.CorrData	0.179	0.003	0.181
getIdMapList.JointIdMap	0.087	0.005	0.092
getMapNames.JointIdMap	0.062	0.005	0.068
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.051	0.002	0.053
getMatchInfo.JointIdMap	0.064	0.002	0.065
getMatchInfo.JointUniquePairs	0.384	0.005	0.388
getMixture.JointUniquePairs	0.123	0.001	0.124
getSampleNames.CorrData	0.002	0.000	0.002
getStats.IdMapCounts	0.233	0.001	0.235
getStats.Mixture	0.002	0.000	0.002
getUnionIdMap.JointIdMap	0.427	0.004	0.431
getUniquePairs.Corr	0.003	0.000	0.003
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.004	0.001	0.003
interactive.corr.boxplot.JointUniquePairs	0.072	0.001	0.074
interactive.corr.plot.JointUniquePairs	0.106	0.006	0.113
interactive.mixture.boxplot.JointUniquePairs	0.172	0.006	0.178
interactive.mixture.plot.JointUniquePairs	0.172	0.007	0.179
interactive.plot.CorrData	0.037	0.001	0.038
interactive.plot.JointUniquePairs	0.000	0.000	0.001
interleave.Misc	0	0	0
line.loess.Display	0.000	0.000	0.001
line.unsorted.Display	0.000	0.000	0.001
logTen.DataFilter	0.106	0.007	0.112
merge.IdMap	0.761	0.004	0.765
minAvgCountConstraint.DataFilter	0.127	0.005	0.132
minCountConstraint.DataFilter	0.190	0.007	0.198
minCountGroupConstraint.DataFilter	0.167	0.012	0.178
mixture.boxplot.JointUniquePairs	0.199	0.001	0.201
mixture.plot.JointUniquePairs	0.144	0.002	0.146
plot.Bootstrap	0.122	0.002	0.125
plot.Corr	0.055	0.002	0.058
plot.CorrData	0.154	0.004	0.158
plot.IdMapCounts	0.292	0.006	0.298
plot.IdMapDiffCounts	0.774	0.003	0.779
plot.Mixture	0.012	0.000	0.014
primaryIDs.IdMapBase	0.002	0.000	0.002
primaryKey.CorrData	0.001	0.000	0.001
primaryKey.IdMapBase	0.002	0.000	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.153	0.008	0.162
secondaryKey.CorrData	0.001	0.001	0.001
secondaryKey.IdMapBase	0.002	0.000	0.003
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.015	0.001	0.016
subsetData.JointUniquePairs	0.049	0.001	0.050
subsetGroups.JointUniquePairs	0.660	0.008	0.667
summary.IdMapDiffCounts	0.287	0.006	0.292
swapKeys.IdMap	0.056	0.000	0.056
swapKeys.UniquePairs	0.062	0.000	0.062
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.036	0.000	0.036
words.Misc	0.002	0.000	0.002
zoom.pars.Display	0.000	0.000	0.001