BioC 2.14: CHECK report for IdMappingAnalysis on petty

Package: IdMappingAnalysis

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.8.0.tar.gz

StartedAt: 2014-10-07 22:35:18 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:38:08 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 170.1 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.8.0’
* 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 ... [13s/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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
getBootstrap.JointUniquePairs 14.241  0.116  14.402
Bootstrap                     13.548  0.155  13.881
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.450	0.027	0.495
Bootstrap	13.548	0.155	13.881
Corr	0.966	0.032	1.005
CorrData	0.170	0.009	0.179
CsvList.merge.Misc	0.007	0.000	0.007
IdMap	0.016	0.000	0.017
IdMapBase	0.002	0.000	0.002
IdMapCounts	1.096	0.016	1.114
IdMapDiff	1.266	0.014	1.282
IdMapDiffCounts	1.152	0.005	1.180
JointIdMap	0.316	0.003	0.320
JointUniquePairs	1.402	0.013	1.418
Mixture	0.375	0.006	0.380
UniquePairs	0.007	0.001	0.007
aligned.IdMapBase	0.054	0.002	0.056
as.IdMap.UniquePairs	0.097	0.000	0.098
as.MultiSet.CorrData	1.381	0.022	1.424
as.UniquePairs.IdMap	0.043	0.000	0.046
as.data.frame.IdMapBase	0.127	0.001	0.138
as.data.frame.JointIdMap	0.308	0.002	0.327
as.list.IdMap	0.031	0.001	0.031
boxplot.JointUniquePairs	0.150	0.003	0.155
byColNames.Subset	0.011	0.001	0.012
byColumn.Subset	0.010	0.001	0.012
byRow.Subset	0.009	0.000	0.009
byRowNames.Subset	0.018	0.000	0.019
clust.Mixture	0.004	0.000	0.004
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.177	0.002	0.183
corr.plot.JointUniquePairs	0.112	0.002	0.116
create.Display	0.001	0.000	0.001
create.UniquePairs	0.246	0.002	0.249
diffCounts.plot.JointIdMap	1.212	0.007	1.243
dim.IdMapBase	0.004	0.000	0.005
dimnames.IdMapBase	0.004	0.000	0.005
do.glm.JointUniquePairs	0.031	0.001	0.033
ecdf.plot.JointIdMap	0.572	0.007	0.581
equals.UniquePairs	0.077	0.001	0.078
fisherTransform.DataFilter	0.001	0.000	0.002
fisherTransformInverse.DataFilter	0.001	0.000	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	14.241	0.116	14.402
getCompoundEvents.IdMapDiffCounts	1.046	0.006	1.066
getCompoundGroups.IdMapDiffCounts	1.054	0.004	1.061
getCorr.JointUniquePairs	0.105	0.002	0.109
getCorrData.JointUniquePairs	0.227	0.002	0.228
getCorrDataFrame.JointUniquePairs	0.046	0.001	0.047
getCounts.IdMap	0.044	0.000	0.045
getCounts.JointIdMap	0.631	0.004	0.637
getData.Corr	0.001	0.001	0.002
getData.Mixture	0.005	0.000	0.005
getDiff.JointIdMap	0.618	0.005	0.624
getExperimentSet.CorrData	0.337	0.008	0.346
getIdMapList.JointIdMap	0.326	0.002	0.328
getMapNames.JointIdMap	0.291	0.003	0.295
getMapNames.JointUniquePairs	0.005	0.000	0.005
getMatch.UniquePairs	0.082	0.002	0.084
getMatchInfo.JointIdMap	0.311	0.006	0.321
getMatchInfo.JointUniquePairs	0.867	0.007	0.874
getMixture.JointUniquePairs	0.284	0.003	0.288
getSampleNames.CorrData	0.005	0.001	0.006
getStats.IdMapCounts	0.541	0.007	0.548
getStats.Mixture	0.007	0.001	0.007
getUnionIdMap.JointIdMap	1.060	0.004	1.065
getUniquePairs.Corr	0.011	0.000	0.011
getUniquePairs.CorrData	0.017	0.001	0.017
getUniquePairs.JointUniquePairs	0.011	0.001	0.011
interactive.corr.boxplot.JointUniquePairs	0.163	0.002	0.165
interactive.corr.plot.JointUniquePairs	0.110	0.011	0.125
interactive.mixture.boxplot.JointUniquePairs	0.388	0.012	0.445
interactive.mixture.plot.JointUniquePairs	0.272	0.012	0.284
interactive.plot.CorrData	0.091	0.001	0.093
interactive.plot.JointUniquePairs	0.001	0.001	0.002
interleave.Misc	0.001	0.000	0.002
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.002	0.000	0.001
logTen.DataFilter	0.197	0.017	0.215
merge.IdMap	1.333	0.004	1.337
minAvgCountConstraint.DataFilter	0.250	0.012	0.261
minCountConstraint.DataFilter	0.228	0.007	0.235
minCountGroupConstraint.DataFilter	0.319	0.011	0.330
mixture.boxplot.JointUniquePairs	0.471	0.009	0.485
mixture.plot.JointUniquePairs	0.284	0.003	0.290
plot.Bootstrap	0.178	0.004	0.183
plot.Corr	0.111	0.003	0.122
plot.CorrData	0.067	0.001	0.070
plot.IdMapCounts	0.541	0.004	0.546
plot.IdMapDiffCounts	1.509	0.008	1.520
plot.Mixture	0.034	0.001	0.036
primaryIDs.IdMapBase	0.006	0.000	0.007
primaryKey.CorrData	0.004	0.001	0.003
primaryKey.IdMapBase	0.007	0.000	0.007
primaryKey.Mixture	0.004	0.001	0.005
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.286	0.008	0.295
secondaryKey.CorrData	0.004	0.001	0.004
secondaryKey.IdMapBase	0.007	0.000	0.006
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.034	0.001	0.034
subsetData.JointUniquePairs	0.020	0.001	0.020
subsetGroups.JointUniquePairs	1.348	0.004	1.354
summary.IdMapDiffCounts	1.195	0.008	1.211
swapKeys.IdMap	0.202	0.001	0.203
swapKeys.UniquePairs	0.038	0.001	0.039
textBoundingBox.Display	0.011	0.000	0.010
to.base.Misc	0.002	0.000	0.003
to.binary.logical.Misc	0.005	0.000	0.005
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.117	0.001	0.119
words.Misc	0.003	0.000	0.003
zoom.pars.Display	0.001	0.000	0.002