Package: IdMappingAnalysis

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.1.1.tar.gz

StartedAt: 2012-06-21 01:01:32 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:03:48 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 136.2 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 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.1.1'
* 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 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
* 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
This is  rChoiceDialogs   1.0.1   2011-01-14 
** help
*** installing help indices
** building package indices
** installing vignettes
   'IdMappingAnalysis.Rnw' using 'latin-9' 
** testing if installed package can be loaded
This is  rChoiceDialogs   1.0.1   2011-01-14 

* DONE (IdMappingAnalysis)

name	user	system	elapsed
000-LB-.IdMapBase	0.516	0.073	0.594
Bootstrap	10.038	0.059	10.160
Corr	0.770	0.016	0.793
CorrData	0.248	0.020	0.270
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.067	0.002	0.069
IdMapBase	0.001	0.001	0.002
IdMapCounts	0.997	0.033	1.042
IdMapDiff	1.148	0.024	1.185
IdMapDiffCounts	0.873	0.019	0.904
JointIdMap	0.259	0.008	0.268
JointUniquePairs	1.168	0.046	1.229
Mixture	0.404	0.010	0.417
UniquePairs	0.003	0.001	0.004
aligned.IdMapBase	0.009	0.001	0.010
as.IdMap.UniquePairs	0.085	0.005	0.091
as.MultiSet.CorrData	1.188	0.050	1.245
as.UniquePairs.IdMap	0.034	0.004	0.038
as.data.frame.IdMapBase	0.188	0.036	0.231
as.data.frame.JointIdMap	0.262	0.008	0.272
as.list.IdMap	0.020	0.003	0.023
boxplot.JointUniquePairs	0.087	0.004	0.091
byColNames.Subset	0.013	0.001	0.014
byColumn.Subset	0.007	0.001	0.007
byRow.Subset	0.019	0.009	0.027
byRowNames.Subset	0.01	0.00	0.01
clust.Mixture	0.000	0.000	0.001
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.104	0.005	0.109
corr.plot.JointUniquePairs	0.079	0.008	0.088
create.Display	0	0	0
create.UniquePairs	0.192	0.017	0.210
diffCounts.plot.JointIdMap	0.874	0.017	0.907
dim.IdMapBase	0.011	0.008	0.021
dimnames.IdMapBase	0.022	0.002	0.024
do.glm.JointUniquePairs	0.115	0.003	0.119
ecdf.plot.JointIdMap	0.473	0.013	0.494
equals.UniquePairs	0.058	0.004	0.063
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	10.482	0.056	10.645
getCompoundEvents.IdMapDiffCounts	0.807	0.018	0.830
getCompoundGroups.IdMapDiffCounts	0.895	0.017	0.946
getCorr.JointUniquePairs	0.085	0.009	0.093
getCorrData.JointUniquePairs	0.296	0.020	0.323
getCorrDataFrame.JointUniquePairs	0.034	0.003	0.036
getCounts.IdMap	0.037	0.001	0.038
getCounts.JointIdMap	0.470	0.013	0.486
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.001	0.001	0.001
getDiff.JointIdMap	0.571	0.013	0.587
getExperimentSet.CorrData	0.390	0.026	0.419
getIdMapList.JointIdMap	0.279	0.010	0.292
getMapNames.JointIdMap	0.260	0.008	0.271
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.065	0.006	0.071
getMatchInfo.JointIdMap	0.270	0.010	0.281
getMatchInfo.JointUniquePairs	0.693	0.002	0.699
getMixture.JointUniquePairs	0.298	0.011	0.310
getSampleNames.CorrData	0.001	0.001	0.002
getStats.IdMapCounts	0.493	0.016	0.511
getStats.Mixture	0.003	0.000	0.003
getUnionIdMap.JointIdMap	0.944	0.021	0.967
getUniquePairs.Corr	0.005	0.001	0.005
getUniquePairs.CorrData	0.005	0.001	0.006
getUniquePairs.JointUniquePairs	0.005	0.001	0.005
interactive.corr.boxplot.JointUniquePairs	0.095	0.005	0.110
interactive.corr.plot.JointUniquePairs	0.078	0.024	0.102
interactive.mixture.boxplot.JointUniquePairs	0.351	0.032	0.385
interactive.mixture.plot.JointUniquePairs	0.289	0.028	0.318
interactive.plot.CorrData	0.096	0.005	0.101
interactive.plot.JointUniquePairs	0.000	0.001	0.001
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
log10.DataFilter	0.024	0.004	0.029
merge.IdMap	1.198	0.017	1.231
minAvgCountConstraint.DataFilter	0.322	0.083	0.407
minCountConstraint.DataFilter	0.233	0.084	0.317
minCountGroupConstraint.DataFilter	0.394	0.087	0.487
mixture.boxplot.JointUniquePairs	0.343	0.015	0.358
mixture.plot.JointUniquePairs	0.286	0.011	0.298
plot.Bootstrap	0.129	0.004	0.133
plot.Corr	0.088	0.009	0.097
plot.CorrData	0.043	0.002	0.046
plot.IdMapCounts	0.499	0.017	0.524
plot.IdMapDiffCounts	1.191	0.023	1.214
plot.Mixture	0.027	0.002	0.029
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.000	0.001	0.001
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.388	0.087	0.480
secondaryKey.CorrData	0.001	0.000	0.001
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.021	0.002	0.024
subsetData.JointUniquePairs	0.010	0.001	0.011
subsetGroups.JointUniquePairs	1.219	0.054	1.354
summary.IdMapDiffCounts	0.790	0.020	0.815
swapKeys.IdMap	0.174	0.009	0.184
swapKeys.UniquePairs	0.030	0.003	0.033
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0	0	0
to.binary.logical.Misc	0.000	0.000	0.001
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.088	0.014	0.102
words.Misc	0	0	0
zoom.pars.Display	0.000	0.001	0.000