BioC 2.14: CHECK report for IdMappingAnalysis on morelia

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 23:33:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:35:30 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 92.9 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_1.8.0.tar.gz
###
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* 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-darwin13.1.0 (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 ... [7s/7s] 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 ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.517  0.049   7.576
Bootstrap                     7.090  0.065   7.156
* 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	0.226	0.012	0.239
Bootstrap	7.090	0.065	7.156
Corr	0.508	0.014	0.523
CorrData	0.059	0.004	0.063
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.009	0.000	0.009
IdMapBase	0.002	0.000	0.001
IdMapCounts	0.404	0.003	0.406
IdMapDiff	0.571	0.002	0.573
IdMapDiffCounts	0.491	0.004	0.495
JointIdMap	0.087	0.001	0.088
JointUniquePairs	0.700	0.005	0.704
Mixture	0.192	0.001	0.193
UniquePairs	0.003	0.000	0.003
aligned.IdMapBase	0.029	0.000	0.029
as.IdMap.UniquePairs	0.044	0.000	0.045
as.MultiSet.CorrData	0.734	0.009	0.749
as.UniquePairs.IdMap	0.023	0.000	0.023
as.data.frame.IdMapBase	0.065	0.001	0.066
as.data.frame.JointIdMap	0.089	0.001	0.091
as.list.IdMap	0.013	0.000	0.014
boxplot.JointUniquePairs	0.081	0.001	0.083
byColNames.Subset	0.006	0.001	0.006
byColumn.Subset	0.006	0.000	0.006
byRow.Subset	0.006	0.000	0.006
byRowNames.Subset	0.007	0.000	0.007
clust.Mixture	0.002	0.000	0.003
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.093	0.001	0.095
corr.plot.JointUniquePairs	0.057	0.001	0.058
create.Display	0.000	0.000	0.001
create.UniquePairs	0.127	0.000	0.128
diffCounts.plot.JointIdMap	0.556	0.002	0.558
dim.IdMapBase	0.001	0.000	0.002
dimnames.IdMapBase	0.001	0.000	0.002
do.glm.JointUniquePairs	0.016	0.000	0.016
ecdf.plot.JointIdMap	0.222	0.004	0.225
equals.UniquePairs	0.046	0.000	0.047
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.000	0.001
getBootstrap.JointUniquePairs	7.517	0.049	7.576
getCompoundEvents.IdMapDiffCounts	0.454	0.007	0.463
getCompoundGroups.IdMapDiffCounts	0.469	0.003	0.471
getCorr.JointUniquePairs	0.060	0.001	0.061
getCorrData.JointUniquePairs	0.093	0.002	0.095
getCorrDataFrame.JointUniquePairs	0.026	0.000	0.027
getCounts.IdMap	0.023	0.001	0.023
getCounts.JointIdMap	0.263	0.002	0.266
getData.Corr	0	0	0
getData.Mixture	0.001	0.000	0.002
getDiff.JointIdMap	0.249	0.004	0.252
getExperimentSet.CorrData	0.182	0.004	0.186
getIdMapList.JointIdMap	0.075	0.001	0.075
getMapNames.JointIdMap	0.075	0.002	0.078
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.044	0.000	0.045
getMatchInfo.JointIdMap	0.094	0.001	0.097
getMatchInfo.JointUniquePairs	0.500	0.003	0.504
getMixture.JointUniquePairs	0.148	0.001	0.149
getSampleNames.CorrData	0.002	0.000	0.002
getStats.IdMapCounts	0.202	0.002	0.205
getStats.Mixture	0.004	0.001	0.005
getUnionIdMap.JointIdMap	0.502	0.001	0.504
getUniquePairs.Corr	0.005	0.000	0.006
getUniquePairs.CorrData	0.011	0.000	0.011
getUniquePairs.JointUniquePairs	0.006	0.000	0.006
interactive.corr.boxplot.JointUniquePairs	0.090	0.001	0.092
interactive.corr.plot.JointUniquePairs	0.040	0.004	0.045
interactive.mixture.boxplot.JointUniquePairs	0.222	0.006	0.233
interactive.mixture.plot.JointUniquePairs	0.159	0.007	0.169
interactive.plot.CorrData	0.042	0.001	0.080
interactive.plot.JointUniquePairs	0.001	0.000	0.000
interleave.Misc	0	0	0
line.loess.Display	0.001	0.000	0.000
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.108	0.009	0.117
merge.IdMap	0.595	0.002	0.599
minAvgCountConstraint.DataFilter	0.130	0.005	0.135
minCountConstraint.DataFilter	0.145	0.004	0.148
minCountGroupConstraint.DataFilter	0.187	0.005	0.191
mixture.boxplot.JointUniquePairs	0.263	0.004	0.267
mixture.plot.JointUniquePairs	0.149	0.004	0.154
plot.Bootstrap	0.076	0.001	0.080
plot.Corr	0.059	0.002	0.062
plot.CorrData	0.034	0.000	0.035
plot.IdMapCounts	0.211	0.000	0.212
plot.IdMapDiffCounts	0.727	0.003	0.732
plot.Mixture	0.021	0.001	0.023
primaryIDs.IdMapBase	0.003	0.000	0.004
primaryKey.CorrData	0.001	0.000	0.002
primaryKey.IdMapBase	0.002	0.000	0.003
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.160	0.004	0.164
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.004	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.000
subsetCorr.JointUniquePairs	0.019	0.000	0.019
subsetData.JointUniquePairs	0.01	0.00	0.01
subsetGroups.JointUniquePairs	0.669	0.007	0.676
summary.IdMapDiffCounts	0.522	0.006	0.528
swapKeys.IdMap	0.071	0.001	0.072
swapKeys.UniquePairs	0.023	0.000	0.023
textBoundingBox.Display	0.005	0.000	0.006
to.base.Misc	0.001	0.000	0.002
to.binary.logical.Misc	0.003	0.000	0.003
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.069	0.000	0.069
words.Misc	0.002	0.001	0.001
zoom.pars.Display	0.000	0.000	0.001