Package: IdMappingAnalysis

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.3.1.tar.gz

StartedAt: 2013-03-25 03:09:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:12:01 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 132.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' version '1.3.1'
* 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 ... [11s/12s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... WARNING
checkRd: (3) CsvList.merge.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) as.list.IdMap.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) boxplotdataJitter.JointUniquePairs.Rd:23: \synopsis will be removed in R 3.1.0
checkRd: (3) byColNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byColumn.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byRow.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) byRowNames.Subset.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) copy.Display.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) create.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) create.UniquePairs.Rd:26: \synopsis will be removed in R 3.1.0
checkRd: (3) do.apply.DataFilter.Rd:27: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransform.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransformInverse.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) fisherTransformJacobean.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) interleave.Misc.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) line.loess.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) line.unsorted.Display.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) log10.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minAvgCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minCountConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) minCountGroupConstraint.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) pack.experiments.CorrData.Rd:21: \synopsis will be removed in R 3.1.0
checkRd: (3) progressMsg.Display.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) removeNASeries.DataFilter.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) swapKeys.IdMap.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) swapKeys.UniquePairs.Rd:19: \synopsis will be removed in R 3.1.0
checkRd: (3) textBoundingBox.Display.Rd:28: \synopsis will be removed in R 3.1.0
checkRd: (3) to.base.Misc.Rd:20: \synopsis will be removed in R 3.1.0
checkRd: (3) to.binary.logical.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) to.index.expr.Misc.Rd:25: \synopsis will be removed in R 3.1.0
checkRd: (3) words.Misc.Rd:22: \synopsis will be removed in R 3.1.0
checkRd: (3) zoom.pars.Display.Rd:20: \synopsis will be removed in R 3.1.0
* 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 examples ... [52s/52s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
getBootstrap.JointUniquePairs 11.278  0.600  11.888
Bootstrap                      8.699  0.539   9.254
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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
   'IdMappingAnalysis.Rnw' using 'latin-9' 
** testing if installed package can be loaded
* DONE (IdMappingAnalysis)

name	user	system	elapsed
000-LB-.IdMapBase	0.402	0.067	0.497
Bootstrap	8.699	0.539	9.254
Corr	0.634	0.019	0.652
CorrData	0.218	0.030	0.250
CsvList.merge.Misc	0.010	0.007	0.016
IdMap	0.016	0.008	0.024
IdMapBase	0.009	0.006	0.014
IdMapCounts	0.747	0.042	0.792
IdMapDiff	0.810	0.032	0.846
IdMapDiffCounts	0.580	0.022	0.601
JointIdMap	0.182	0.014	0.196
JointUniquePairs	0.820	0.039	0.861
Mixture	0.284	0.012	0.296
UniquePairs	0.012	0.008	0.021
aligned.IdMapBase	0.020	0.012	0.032
as.IdMap.UniquePairs	0.061	0.009	0.070
as.MultiSet.CorrData	0.952	0.055	1.009
as.UniquePairs.IdMap	0.031	0.011	0.042
as.data.frame.IdMapBase	0.092	0.034	0.127
as.data.frame.JointIdMap	0.195	0.015	0.210
as.list.IdMap	0.022	0.009	0.030
boxplot.JointUniquePairs	0.150	0.021	0.172
byColNames.Subset	0.011	0.010	0.021
byColumn.Subset	0.013	0.011	0.029
byRow.Subset	0.014	0.015	0.028
byRowNames.Subset	0.017	0.010	0.028
clust.Mixture	0.006	0.007	0.013
copy.Display	0.009	0.007	0.016
corr.boxplot.JointUniquePairs	0.103	0.021	0.124
corr.plot.JointUniquePairs	0.075	0.017	0.093
create.Display	0.005	0.006	0.011
create.UniquePairs	0.136	0.016	0.152
diffCounts.plot.JointIdMap	0.662	0.025	0.688
dim.IdMapBase	0.011	0.009	0.020
dimnames.IdMapBase	0.025	0.014	0.039
do.glm.JointUniquePairs	0.032	0.010	0.043
ecdf.plot.JointIdMap	0.365	0.021	0.386
equals.UniquePairs	0.053	0.015	0.068
fisherTransform.DataFilter	0.007	0.006	0.013
fisherTransformInverse.DataFilter	0.005	0.007	0.013
fisherTransformJacobean.DataFilter	0.005	0.007	0.012
getBootstrap.JointUniquePairs	11.278	0.600	11.888
getCompoundEvents.IdMapDiffCounts	0.621	0.023	0.645
getCompoundGroups.IdMapDiffCounts	1.004	0.032	1.036
getCorr.JointUniquePairs	0.114	0.017	0.133
getCorrData.JointUniquePairs	0.402	0.035	0.437
getCorrDataFrame.JointUniquePairs	0.043	0.011	0.054
getCounts.IdMap	0.053	0.009	0.062
getCounts.JointIdMap	0.561	0.020	0.580
getData.Corr	0.008	0.008	0.017
getData.Mixture	0.010	0.008	0.017
getDiff.JointIdMap	0.676	0.020	0.697
getExperimentSet.CorrData	0.307	0.031	0.339
getIdMapList.JointIdMap	0.343	0.019	0.363
getMapNames.JointIdMap	0.323	0.016	0.339
getMapNames.JointUniquePairs	0.010	0.007	0.016
getMatch.UniquePairs	0.092	0.017	0.107
getMatchInfo.JointIdMap	0.337	0.018	0.356
getMatchInfo.JointUniquePairs	0.775	0.009	0.783
getMixture.JointUniquePairs	0.319	0.022	0.342
getSampleNames.CorrData	0.009	0.008	0.016
getStats.IdMapCounts	0.605	0.025	0.633
getStats.Mixture	0.011	0.006	0.018
getUnionIdMap.JointIdMap	1.183	0.025	1.209
getUniquePairs.Corr	0.021	0.009	0.032
getUniquePairs.CorrData	0.011	0.006	0.017
getUniquePairs.JointUniquePairs	0.015	0.008	0.022
interactive.corr.boxplot.JointUniquePairs	0.113	0.025	0.140
interactive.corr.plot.JointUniquePairs	0.115	0.113	0.230
interactive.mixture.boxplot.JointUniquePairs	0.442	0.100	0.542
interactive.mixture.plot.JointUniquePairs	0.430	0.087	0.521
interactive.plot.CorrData	0.090	0.016	0.107
interactive.plot.JointUniquePairs	0.008	0.010	0.018
interleave.Misc	0.007	0.007	0.014
line.loess.Display	0.008	0.009	0.017
line.unsorted.Display	0.008	0.009	0.017
log10.DataFilter	0.037	0.016	0.054
merge.IdMap	1.436	0.031	1.470
minAvgCountConstraint.DataFilter	0.270	0.082	0.352
minCountConstraint.DataFilter	0.286	0.086	0.372
minCountGroupConstraint.DataFilter	0.379	0.083	0.463
mixture.boxplot.JointUniquePairs	0.375	0.028	0.403
mixture.plot.JointUniquePairs	0.210	0.017	0.230
plot.Bootstrap	0.114	0.012	0.130
plot.Corr	0.122	0.024	0.147
plot.CorrData	0.041	0.010	0.050
plot.IdMapCounts	0.352	0.021	0.373
plot.IdMapDiffCounts	0.887	0.032	0.922
plot.Mixture	0.039	0.011	0.051
primaryIDs.IdMapBase	0.018	0.008	0.025
primaryKey.CorrData	0.007	0.007	0.014
primaryKey.IdMapBase	0.008	0.008	0.016
primaryKey.Mixture	0.007	0.007	0.014
progressMsg.Display	0.006	0.007	0.013
removeNASeries.DataFilter	0.205	0.059	0.263
secondaryKey.CorrData	0.004	0.005	0.008
secondaryKey.IdMapBase	0.006	0.005	0.011
secondaryKey.Mixture	0.003	0.005	0.006
subsetCorr.JointUniquePairs	0.024	0.009	0.033
subsetData.JointUniquePairs	0.020	0.014	0.039
subsetGroups.JointUniquePairs	1.409	0.062	1.473
summary.IdMapDiffCounts	0.995	0.030	1.027
swapKeys.IdMap	0.247	0.023	0.270
swapKeys.UniquePairs	0.058	0.016	0.074
textBoundingBox.Display	0.009	0.007	0.016
to.base.Misc	0.010	0.008	0.018
to.binary.logical.Misc	0.011	0.008	0.019
to.index.expr.Misc	0.009	0.008	0.017
unique.UniquePairs	0.154	0.030	0.185
words.Misc	0.004	0.005	0.010
zoom.pars.Display	0.008	0.008	0.016