BioC 3.3: CHECK report for IdMappingAnalysis on morelia

Package: IdMappingAnalysis

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.15.0.tar.gz

StartedAt: 2016-04-21 04:02:05 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 04:03:36 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 90.7 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_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.15.0’
* 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 ... [6s/7s] 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 ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.159  0.063   7.360
Bootstrap                     6.903  0.079   7.199
* 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	0.236	0.015	0.262
Bootstrap	6.903	0.079	7.199
Corr	0.383	0.015	0.402
CorrData	0.059	0.005	0.063
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.009	0.000	0.009
IdMapBase	0.002	0.000	0.003
IdMapCounts	0.461	0.011	0.477
IdMapDiff	0.518	0.006	0.530
IdMapDiffCounts	0.434	0.008	0.446
JointIdMap	0.083	0.002	0.084
JointUniquePairs	0.789	0.003	0.803
Mixture	0.203	0.001	0.278
UniquePairs	0.004	0.000	0.003
aligned.IdMapBase	0.008	0.000	0.008
as.IdMap.UniquePairs	0.048	0.001	0.049
as.MultiSet.CorrData	0.687	0.008	0.695
as.UniquePairs.IdMap	0.025	0.001	0.026
as.data.frame.IdMapBase	0.074	0.001	0.075
as.data.frame.JointIdMap	0.073	0.003	0.075
as.list.IdMap	0.015	0.000	0.016
boxplot.JointUniquePairs	0.069	0.001	0.076
byColNames.Subset	0.005	0.001	0.006
byColumn.Subset	0.005	0.000	0.006
byRow.Subset	0.005	0.001	0.005
byRowNames.Subset	0.008	0.000	0.009
clust.Mixture	0.002	0.000	0.003
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.098	0.002	0.103
corr.plot.JointUniquePairs	0.056	0.002	0.059
create.Display	0.000	0.000	0.001
create.UniquePairs	0.156	0.000	0.160
diffCounts.plot.JointIdMap	0.576	0.006	0.595
dim.IdMapBase	0.003	0.000	0.003
dimnames.IdMapBase	0.002	0.000	0.005
do.glm.JointUniquePairs	0.018	0.001	0.024
ecdf.plot.JointIdMap	0.232	0.001	0.259
equals.UniquePairs	0.048	0.000	0.049
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0.001	0.001	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	7.159	0.063	7.360
getCompoundEvents.IdMapDiffCounts	0.443	0.003	0.466
getCompoundGroups.IdMapDiffCounts	0.482	0.006	0.490
getCorr.JointUniquePairs	0.056	0.002	0.058
getCorrData.JointUniquePairs	0.076	0.001	0.076
getCorrDataFrame.JointUniquePairs	0.025	0.001	0.025
getCounts.IdMap	0.027	0.000	0.030
getCounts.JointIdMap	0.215	0.002	0.218
getData.Corr	0.001	0.000	0.002
getData.Mixture	0.002	0.000	0.003
getDiff.JointIdMap	0.315	0.008	0.323
getExperimentSet.CorrData	0.106	0.004	0.112
getIdMapList.JointIdMap	0.085	0.001	0.087
getMapNames.JointIdMap	0.077	0.001	0.077
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.064	0.001	0.064
getMatchInfo.JointIdMap	0.092	0.003	0.096
getMatchInfo.JointUniquePairs	0.433	0.001	0.484
getMixture.JointUniquePairs	0.164	0.002	0.167
getSampleNames.CorrData	0.003	0.000	0.004
getStats.IdMapCounts	0.218	0.005	0.222
getStats.Mixture	0.004	0.000	0.004
getUnionIdMap.JointIdMap	0.515	0.005	0.524
getUniquePairs.Corr	0.006	0.001	0.006
getUniquePairs.CorrData	0.006	0.000	0.006
getUniquePairs.JointUniquePairs	0.006	0.001	0.007
interactive.corr.boxplot.JointUniquePairs	0.090	0.003	0.094
interactive.corr.plot.JointUniquePairs	0.058	0.006	0.065
interactive.mixture.boxplot.JointUniquePairs	0.211	0.007	0.220
interactive.mixture.plot.JointUniquePairs	0.163	0.008	0.171
interactive.plot.CorrData	0.041	0.001	0.043
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.001	0.000
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.176	0.012	0.191
merge.IdMap	0.752	0.004	0.760
minAvgCountConstraint.DataFilter	0.109	0.007	0.116
minCountConstraint.DataFilter	0.132	0.006	0.141
minCountGroupConstraint.DataFilter	0.165	0.006	0.171
mixture.boxplot.JointUniquePairs	0.224	0.002	0.227
mixture.plot.JointUniquePairs	0.161	0.002	0.164
plot.Bootstrap	0.086	0.002	0.090
plot.Corr	0.064	0.002	0.067
plot.CorrData	0.029	0.001	0.029
plot.IdMapCounts	0.222	0.001	0.435
plot.IdMapDiffCounts	0.715	0.004	0.723
plot.Mixture	0.020	0.001	0.022
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.003	0.000	0.004
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.148	0.005	0.153
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.024	0.001	0.025
subsetData.JointUniquePairs	0.011	0.000	0.012
subsetGroups.JointUniquePairs	0.724	0.003	0.747
summary.IdMapDiffCounts	0.471	0.002	0.476
swapKeys.IdMap	0.074	0.001	0.075
swapKeys.UniquePairs	0.026	0.001	0.027
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.082	0.001	0.083
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0.000	0.000	0.001