BioC 3.0: CHECK report for IdMappingAnalysis on perceval

Package: IdMappingAnalysis

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.10.0.tar.gz

StartedAt: 2015-04-10 02:51:22 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:53:20 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 117.6 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 --no-multiarch IdMappingAnalysis_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.10.0’
* 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 ... [8s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
as.data.frame.IdMapBase: no visible global function definition for
  ‘getName’
as.data.frame.IdMapBase: no visible global function definition for
  ‘throw’
as.IdMap.UniquePairs: no visible global function definition for
  ‘getName’
as.list.IdMap: no visible global function definition for ‘throw’
Bootstrap: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
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’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
Display: no visible global function definition for ‘extend’
Display: no visible global function definition for ‘Object’
ecdf.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
getCorr.JointUniquePairs: no visible global function definition for
  ‘equals’
getExperimentSet.CorrData: no visible global function definition for
  ‘throw’
getIdMapList.JointIdMap: no visible global function definition for
  ‘throw’
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’
interactive.plot.CorrData: no visible global function definition for
  ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘rselect.list’
JointIdMap: no visible global function definition for ‘extend’
JointUniquePairs: no visible global function definition for ‘extend’
merge.IdMap: no visible global function definition for ‘getName’
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’
Subset: no visible global function definition for ‘extend’
Subset: no visible global function definition for ‘Object’
unique.UniquePairs: no visible global function definition for ‘getName’
UniquePairs: no visible global function definition for ‘throw’
UniquePairs: no visible global function definition for ‘extend’
* 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 ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 9.221  0.123   9.356
Bootstrap                     8.124  0.127   8.272
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.382	0.024	0.407
Bootstrap	8.124	0.127	8.272
Corr	0.577	0.029	0.606
CorrData	0.104	0.002	0.106
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.010	0.001	0.010
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.670	0.025	0.694
IdMapDiff	0.775	0.008	0.782
IdMapDiffCounts	0.748	0.002	0.751
JointIdMap	0.201	0.010	0.210
JointUniquePairs	0.841	0.009	0.850
Mixture	0.252	0.002	0.255
UniquePairs	0.005	0.001	0.006
aligned.IdMapBase	0.010	0.001	0.010
as.IdMap.UniquePairs	0.069	0.000	0.069
as.MultiSet.CorrData	0.999	0.017	1.019
as.UniquePairs.IdMap	0.025	0.000	0.024
as.data.frame.IdMapBase	0.077	0.001	0.078
as.data.frame.JointIdMap	0.172	0.004	0.177
as.list.IdMap	0.038	0.000	0.038
boxplot.JointUniquePairs	0.094	0.004	0.098
byColNames.Subset	0.007	0.000	0.007
byColumn.Subset	0.007	0.001	0.007
byRow.Subset	0.005	0.000	0.006
byRowNames.Subset	0.013	0.000	0.013
clust.Mixture	0.002	0.000	0.003
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.111	0.003	0.122
corr.plot.JointUniquePairs	0.069	0.002	0.079
create.Display	0.001	0.001	0.001
create.UniquePairs	0.146	0.001	0.227
diffCounts.plot.JointIdMap	0.829	0.004	0.939
dim.IdMapBase	0.002	0.000	0.003
dimnames.IdMapBase	0.002	0.000	0.003
do.glm.JointUniquePairs	0.019	0.000	0.020
ecdf.plot.JointIdMap	0.428	0.011	0.462
equals.UniquePairs	0.045	0.001	0.046
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.000
getBootstrap.JointUniquePairs	9.221	0.123	9.356
getCompoundEvents.IdMapDiffCounts	0.623	0.017	0.641
getCompoundGroups.IdMapDiffCounts	0.651	0.007	0.658
getCorr.JointUniquePairs	0.064	0.002	0.078
getCorrData.JointUniquePairs	0.139	0.007	0.146
getCorrDataFrame.JointUniquePairs	0.026	0.000	0.026
getCounts.IdMap	0.024	0.000	0.024
getCounts.JointIdMap	0.428	0.011	0.437
getData.Corr	0.001	0.000	0.002
getData.Mixture	0.003	0.001	0.003
getDiff.JointIdMap	0.385	0.005	0.390
getExperimentSet.CorrData	0.321	0.011	0.332
getIdMapList.JointIdMap	0.194	0.003	0.197
getMapNames.JointIdMap	0.171	0.007	0.178
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.051	0.001	0.051
getMatchInfo.JointIdMap	0.192	0.003	0.195
getMatchInfo.JointUniquePairs	0.446	0.002	0.446
getMixture.JointUniquePairs	0.183	0.004	0.196
getSampleNames.CorrData	0.003	0.001	0.003
getStats.IdMapCounts	0.316	0.005	0.321
getStats.Mixture	0.003	0.000	0.004
getUnionIdMap.JointIdMap	0.666	0.006	0.671
getUniquePairs.Corr	0.007	0.000	0.007
getUniquePairs.CorrData	0.007	0.001	0.007
getUniquePairs.JointUniquePairs	0.007	0.000	0.008
interactive.corr.boxplot.JointUniquePairs	0.096	0.002	0.098
interactive.corr.plot.JointUniquePairs	0.092	0.012	0.103
interactive.mixture.boxplot.JointUniquePairs	0.243	0.014	0.257
interactive.mixture.plot.JointUniquePairs	0.184	0.014	0.198
interactive.plot.CorrData	0.077	0.003	0.091
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.000	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.130	0.012	0.142
merge.IdMap	0.936	0.013	0.948
minAvgCountConstraint.DataFilter	0.138	0.009	0.147
minCountConstraint.DataFilter	0.181	0.013	0.195
minCountGroupConstraint.DataFilter	0.233	0.012	0.246
mixture.boxplot.JointUniquePairs	0.259	0.002	0.268
mixture.plot.JointUniquePairs	0.202	0.008	0.221
plot.Bootstrap	0.096	0.004	0.111
plot.Corr	0.075	0.003	0.095
plot.CorrData	0.057	0.002	0.069
plot.IdMapCounts	0.354	0.004	0.367
plot.IdMapDiffCounts	1.009	0.005	1.021
plot.Mixture	0.021	0.001	0.030
primaryIDs.IdMapBase	0.004	0.000	0.005
primaryKey.CorrData	0.002	0.000	0.003
primaryKey.IdMapBase	0.004	0.000	0.005
primaryKey.Mixture	0.003	0.000	0.003
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.334	0.010	0.343
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.004	0.000	0.004
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.019	0.001	0.020
subsetData.JointUniquePairs	0.013	0.001	0.014
subsetGroups.JointUniquePairs	0.792	0.009	0.799
summary.IdMapDiffCounts	0.649	0.015	0.663
swapKeys.IdMap	0.124	0.001	0.126
swapKeys.UniquePairs	0.024	0.000	0.026
textBoundingBox.Display	0.000	0.001	0.001
to.base.Misc	0.002	0.000	0.002
to.binary.logical.Misc	0.003	0.000	0.004
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.086	0.000	0.086
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0	0	0