BioC 2.13: CHECK report for IdMappingAnalysis on perceval

Package: IdMappingAnalysis

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.6.0.tar.gz

StartedAt: 2014-04-05 02:05:52 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:08:04 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 131.6 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.6.0’
* 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 ... [10s/10s] 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 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 ... [52s/54s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
getBootstrap.JointUniquePairs 11.432  0.413  12.024
Bootstrap                     10.270  0.286  11.054
* 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-2.13-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	0.606	0.041	0.648
Bootstrap	10.270	0.286	11.054
Corr	0.648	0.035	0.721
CorrData	0.351	0.019	0.375
CsvList.merge.Misc	0.013	0.004	0.017
IdMap	0.018	0.005	0.024
IdMapBase	0.008	0.004	0.012
IdMapCounts	0.785	0.027	0.834
IdMapDiff	1.032	0.025	1.078
IdMapDiffCounts	0.742	0.015	0.785
JointIdMap	0.221	0.006	0.231
JointUniquePairs	1.085	0.027	1.126
Mixture	0.278	0.007	0.289
UniquePairs	0.019	0.003	0.022
aligned.IdMapBase	0.044	0.004	0.048
as.IdMap.UniquePairs	0.093	0.003	0.095
as.MultiSet.CorrData	1.313	0.054	1.368
as.UniquePairs.IdMap	0.049	0.004	0.056
as.data.frame.IdMapBase	0.254	0.014	0.269
as.data.frame.JointIdMap	0.211	0.006	0.226
as.list.IdMap	0.034	0.002	0.036
boxplot.JointUniquePairs	0.101	0.013	0.115
byColNames.Subset	0.026	0.006	0.033
byColumn.Subset	0.028	0.006	0.036
byRow.Subset	0.027	0.003	0.031
byRowNames.Subset	0.026	0.003	0.030
clust.Mixture	0.014	0.002	0.016
copy.Display	0.010	0.006	0.016
corr.boxplot.JointUniquePairs	0.128	0.016	0.149
corr.plot.JointUniquePairs	0.079	0.009	0.089
create.Display	0.008	0.004	0.011
create.UniquePairs	0.141	0.007	0.148
diffCounts.plot.JointIdMap	0.867	0.017	0.895
dim.IdMapBase	0.023	0.010	0.033
dimnames.IdMapBase	0.180	0.011	0.201
do.glm.JointUniquePairs	0.037	0.004	0.042
ecdf.plot.JointIdMap	0.457	0.011	0.511
equals.UniquePairs	0.069	0.010	0.079
fisherTransform.DataFilter	0.008	0.004	0.013
fisherTransformInverse.DataFilter	0.008	0.005	0.014
fisherTransformJacobean.DataFilter	0.009	0.005	0.013
getBootstrap.JointUniquePairs	11.432	0.413	12.024
getCompoundEvents.IdMapDiffCounts	0.748	0.021	0.782
getCompoundGroups.IdMapDiffCounts	0.914	0.020	0.965
getCorr.JointUniquePairs	0.087	0.008	0.108
getCorrData.JointUniquePairs	0.342	0.020	0.369
getCorrDataFrame.JointUniquePairs	0.049	0.007	0.056
getCounts.IdMap	0.040	0.007	0.048
getCounts.JointIdMap	0.359	0.014	0.376
getData.Corr	0.011	0.005	0.015
getData.Mixture	0.014	0.006	0.019
getDiff.JointIdMap	0.460	0.007	0.467
getExperimentSet.CorrData	0.355	0.035	0.389
getIdMapList.JointIdMap	0.325	0.013	0.339
getMapNames.JointIdMap	0.203	0.015	0.219
getMapNames.JointUniquePairs	0.015	0.009	0.024
getMatch.UniquePairs	0.070	0.011	0.082
getMatchInfo.JointIdMap	0.196	0.008	0.208
getMatchInfo.JointUniquePairs	0.515	0.007	0.522
getMixture.JointUniquePairs	0.208	0.012	0.225
getSampleNames.CorrData	0.015	0.007	0.022
getStats.IdMapCounts	0.411	0.017	0.428
getStats.Mixture	0.016	0.005	0.024
getUnionIdMap.JointIdMap	0.779	0.020	0.856
getUniquePairs.Corr	0.019	0.006	0.025
getUniquePairs.CorrData	0.010	0.004	0.015
getUniquePairs.JointUniquePairs	0.018	0.008	0.028
interactive.corr.boxplot.JointUniquePairs	0.136	0.019	0.183
interactive.corr.plot.JointUniquePairs	0.101	0.017	0.140
interactive.mixture.boxplot.JointUniquePairs	0.287	0.027	0.323
interactive.mixture.plot.JointUniquePairs	0.265	0.021	0.289
interactive.plot.CorrData	0.098	0.014	0.122
interactive.plot.JointUniquePairs	0.012	0.007	0.023
interleave.Misc	0.010	0.004	0.014
line.loess.Display	0.003	0.004	0.007
line.unsorted.Display	0.009	0.007	0.015
logTen.DataFilter	0.218	0.032	0.252
merge.IdMap	0.924	0.012	0.956
minAvgCountConstraint.DataFilter	0.228	0.019	0.246
minCountConstraint.DataFilter	0.229	0.033	0.266
minCountGroupConstraint.DataFilter	0.290	0.035	0.329
mixture.boxplot.JointUniquePairs	0.278	0.017	0.295
mixture.plot.JointUniquePairs	0.199	0.007	0.207
plot.Bootstrap	0.115	0.008	0.123
plot.Corr	0.097	0.010	0.108
plot.CorrData	0.060	0.006	0.067
plot.IdMapCounts	0.401	0.013	0.421
plot.IdMapDiffCounts	1.237	0.028	1.437
plot.Mixture	0.036	0.008	0.047
primaryIDs.IdMapBase	0.015	0.007	0.027
primaryKey.CorrData	0.005	0.003	0.009
primaryKey.IdMapBase	0.007	0.006	0.013
primaryKey.Mixture	0.012	0.006	0.034
progressMsg.Display	0.009	0.005	0.015
removeNASeries.DataFilter	0.253	0.025	0.316
secondaryKey.CorrData	0.013	0.004	0.025
secondaryKey.IdMapBase	0.016	0.005	0.020
secondaryKey.Mixture	0.012	0.005	0.017
subsetCorr.JointUniquePairs	0.042	0.007	0.058
subsetData.JointUniquePairs	0.036	0.012	0.049
subsetGroups.JointUniquePairs	1.022	0.012	1.130
summary.IdMapDiffCounts	0.846	0.016	0.896
swapKeys.IdMap	0.168	0.006	0.175
swapKeys.UniquePairs	0.070	0.005	0.075
textBoundingBox.Display	0.013	0.003	0.015
to.base.Misc	0.015	0.004	0.018
to.binary.logical.Misc	0.011	0.005	0.015
to.index.expr.Misc	0.003	0.003	0.006
unique.UniquePairs	0.093	0.012	0.107
words.Misc	0.003	0.005	0.009
zoom.pars.Display	0.009	0.006	0.015