Package: IdMappingAnalysis

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.2.1.tar.gz

StartedAt: 2013-03-25 00:03:59 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:05:47 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 108.3 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.2.1'
* 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 whether package 'IdMappingAnalysis' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... OK
* checking Rd files ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 8.633  0.051   8.775
Bootstrap                     7.858  0.048   8.000
* 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

* 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	0.491	0.067	0.561
Bootstrap	7.858	0.048	8.000
Corr	0.582	0.012	0.607
CorrData	0.230	0.027	0.258
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.007	0.000	0.008
IdMapBase	0.002	0.000	0.001
IdMapCounts	0.787	0.025	0.812
IdMapDiff	0.815	0.020	0.840
IdMapDiffCounts	0.625	0.013	0.638
JointIdMap	0.196	0.009	0.204
JointUniquePairs	0.914	0.041	0.958
Mixture	0.283	0.013	0.296
UniquePairs	0.003	0.001	0.002
aligned.IdMapBase	0.007	0.000	0.007
as.IdMap.UniquePairs	0.064	0.004	0.069
as.MultiSet.CorrData	1.007	0.053	1.064
as.UniquePairs.IdMap	0.029	0.003	0.031
as.data.frame.IdMapBase	0.161	0.030	0.192
as.data.frame.JointIdMap	0.184	0.007	0.192
as.list.IdMap	0.016	0.003	0.019
boxplot.JointUniquePairs	0.074	0.004	0.078
byColNames.Subset	0.006	0.000	0.006
byColumn.Subset	0.011	0.000	0.012
byRow.Subset	0.015	0.008	0.024
byRowNames.Subset	0.008	0.001	0.009
clust.Mixture	0.001	0.000	0.001
copy.Display	0.000	0.001	0.000
corr.boxplot.JointUniquePairs	0.081	0.006	0.088
corr.plot.JointUniquePairs	0.063	0.009	0.073
create.Display	0	0	0
create.UniquePairs	0.155	0.016	0.176
diffCounts.plot.JointIdMap	0.773	0.024	0.801
dim.IdMapBase	0.009	0.007	0.016
dimnames.IdMapBase	0.015	0.003	0.018
do.glm.JointUniquePairs	0.024	0.002	0.026
ecdf.plot.JointIdMap	0.360	0.011	0.373
equals.UniquePairs	0.050	0.005	0.055
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0.000	0.001	0.001
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	8.633	0.051	8.775
getCompoundEvents.IdMapDiffCounts	0.598	0.019	0.624
getCompoundGroups.IdMapDiffCounts	0.606	0.015	0.622
getCorr.JointUniquePairs	0.062	0.008	0.079
getCorrData.JointUniquePairs	0.345	0.025	0.373
getCorrDataFrame.JointUniquePairs	0.021	0.002	0.023
getCounts.IdMap	0.027	0.001	0.028
getCounts.JointIdMap	0.339	0.011	0.349
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.001	0.001
getDiff.JointIdMap	0.398	0.011	0.412
getExperimentSet.CorrData	0.241	0.019	0.261
getIdMapList.JointIdMap	0.204	0.009	0.214
getMapNames.JointIdMap	0.193	0.008	0.202
getMapNames.JointUniquePairs	0.001	0.000	0.002
getMatch.UniquePairs	0.056	0.006	0.063
getMatchInfo.JointIdMap	0.192	0.007	0.201
getMatchInfo.JointUniquePairs	0.486	0.001	0.488
getMixture.JointUniquePairs	0.196	0.011	0.206
getSampleNames.CorrData	0.001	0.001	0.001
getStats.IdMapCounts	0.389	0.022	0.420
getStats.Mixture	0.002	0.000	0.003
getUnionIdMap.JointIdMap	0.698	0.017	0.722
getUniquePairs.Corr	0.004	0.000	0.005
getUniquePairs.CorrData	0.005	0.000	0.005
getUniquePairs.JointUniquePairs	0.011	0.001	0.013
interactive.corr.boxplot.JointUniquePairs	0.084	0.006	0.092
interactive.corr.plot.JointUniquePairs	0.073	0.134	0.224
interactive.mixture.boxplot.JointUniquePairs	0.241	0.097	0.342
interactive.mixture.plot.JointUniquePairs	0.196	0.144	0.377
interactive.plot.CorrData	0.050	0.004	0.054
interactive.plot.JointUniquePairs	0.000	0.001	0.000
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0	0	0
line.unsorted.Display	0.000	0.001	0.000
log10.DataFilter	0.045	0.006	0.053
merge.IdMap	0.975	0.015	0.991
minAvgCountConstraint.DataFilter	0.155	0.058	0.215
minCountConstraint.DataFilter	0.200	0.075	0.282
minCountGroupConstraint.DataFilter	0.247	0.076	0.343
mixture.boxplot.JointUniquePairs	0.244	0.012	0.279
mixture.plot.JointUniquePairs	0.195	0.011	0.218
plot.Bootstrap	0.105	0.007	0.125
plot.Corr	0.071	0.010	0.091
plot.CorrData	0.044	0.003	0.049
plot.IdMapCounts	0.371	0.015	0.420
plot.IdMapDiffCounts	0.976	0.032	1.052
plot.Mixture	0.023	0.004	0.029
primaryIDs.IdMapBase	0.002	0.000	0.003
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.003	0.000	0.002
primaryKey.Mixture	0.001	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.201	0.070	0.301
secondaryKey.CorrData	0.001	0.000	0.001
secondaryKey.IdMapBase	0.002	0.001	0.003
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.021	0.003	0.028
subsetData.JointUniquePairs	0.009	0.000	0.012
subsetGroups.JointUniquePairs	0.921	0.049	0.990
summary.IdMapDiffCounts	0.593	0.020	0.616
swapKeys.IdMap	0.124	0.008	0.132
swapKeys.UniquePairs	0.022	0.002	0.025
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.000	0.001	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.079	0.016	0.096
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0	0	0