Package: IdMappingAnalysis

Version: 1.0.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.0.0.tar.gz

StartedAt: 2012-04-01 01:42:46 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:43:56 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 70.0 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' version '1.0.0'
* 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 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 ... NOTE
Mixture: warning in Mclust(corrData, G = G, model = "V"): partial
  argument match of 'model' to 'modelNames'
* 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 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-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
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	0.320	0.020	0.338
Bootstrap	5.524	0.008	5.536
Corr	0.44	0.00	0.44
CorrData	0.084	0.004	0.087
CsvList.merge.Misc	0.004	0.000	0.001
IdMap	0.004	0.000	0.003
IdMapBase	0	0	0
IdMapCounts	0.296	0.000	0.294
IdMapDiff	0.504	0.000	0.510
IdMapDiffCounts	0.312	0.000	0.312
JointIdMap	0.060	0.000	0.061
JointUniquePairs	0.544	0.004	0.546
Mixture	0.348	0.000	0.349
UniquePairs	0.000	0.004	0.001
aligned.IdMapBase	0.004	0.000	0.005
as.IdMap.UniquePairs	0.032	0.000	0.031
as.MultiSet.CorrData	0.656	0.008	0.694
as.UniquePairs.IdMap	0.064	0.000	0.065
as.data.frame.IdMapBase	0.060	0.000	0.063
as.data.frame.JointIdMap	0.060	0.000	0.058
as.list.IdMap	0.012	0.000	0.012
boxplot.JointUniquePairs	0.052	0.000	0.050
byColNames.Subset	0.008	0.000	0.007
byColumn.Subset	0.004	0.000	0.004
byRow.Subset	0.004	0.000	0.006
byRowNames.Subset	0.004	0.000	0.004
clust.Mixture	0	0	0
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.116	0.000	0.116
corr.plot.JointUniquePairs	0.044	0.000	0.045
create.Display	0.000	0.000	0.001
create.UniquePairs	0.060	0.000	0.062
diffCounts.plot.JointIdMap	0.416	0.000	0.413
dim.IdMapBase	0.004	0.000	0.006
dimnames.IdMapBase	0.064	0.000	0.066
do.glm.JointUniquePairs	0.020	0.000	0.017
ecdf.plot.JointIdMap	0.168	0.000	0.168
equals.UniquePairs	0.020	0.000	0.019
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	5.857	0.008	5.862
getCompoundEvents.IdMapDiffCounts	0.284	0.000	0.284
getCompoundGroups.IdMapDiffCounts	0.356	0.000	0.357
getCorr.JointUniquePairs	0.044	0.000	0.043
getCorrData.JointUniquePairs	0.12	0.00	0.12
getCorrDataFrame.JointUniquePairs	0.012	0.000	0.016
getCounts.IdMap	0.012	0.000	0.015
getCounts.JointIdMap	0.132	0.000	0.128
getData.Corr	0	0	0
getData.Mixture	0	0	0
getDiff.JointIdMap	0.204	0.000	0.204
getExperimentSet.CorrData	0.152	0.004	0.157
getIdMapList.JointIdMap	0.116	0.000	0.115
getMapNames.JointIdMap	0.052	0.000	0.054
getMapNames.JointUniquePairs	0.004	0.000	0.001
getMatch.UniquePairs	0.020	0.000	0.021
getMatchInfo.JointIdMap	0.052	0.000	0.054
getMatchInfo.JointUniquePairs	0.408	0.000	0.408
getMixture.JointUniquePairs	0.208	0.000	0.208
getSampleNames.CorrData	0.000	0.000	0.001
getStats.IdMapCounts	0.156	0.000	0.157
getStats.Mixture	0.000	0.000	0.003
getUnionIdMap.JointIdMap	0.428	0.000	0.428
getUniquePairs.Corr	0.004	0.000	0.003
getUniquePairs.CorrData	0.004	0.000	0.003
getUniquePairs.JointUniquePairs	0.004	0.000	0.003
interactive.corr.boxplot.JointUniquePairs	0.068	0.000	0.067
interactive.corr.plot.JointUniquePairs	0.044	0.004	0.048
interactive.mixture.boxplot.JointUniquePairs	0.264	0.004	0.267
interactive.mixture.plot.JointUniquePairs	0.248	0.000	0.247
interactive.plot.CorrData	0.044	0.000	0.042
interactive.plot.JointUniquePairs	0	0	0
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
log10.DataFilter	0.016	0.004	0.021
merge.IdMap	0.648	0.000	0.649
minAvgCountConstraint.DataFilter	0.132	0.004	0.133
minCountConstraint.DataFilter	0.212	0.000	0.211
minCountGroupConstraint.DataFilter	0.24	0.00	0.24
mixture.boxplot.JointUniquePairs	0.248	0.000	0.246
mixture.plot.JointUniquePairs	0.208	0.000	0.208
plot.Bootstrap	0.072	0.000	0.072
plot.Corr	0.048	0.004	0.051
plot.CorrData	0.028	0.000	0.027
plot.IdMapCounts	0.152	0.000	0.151
plot.IdMapDiffCounts	0.704	0.000	0.706
plot.Mixture	0.02	0.00	0.02
primaryIDs.IdMapBase	0.000	0.000	0.001
primaryKey.CorrData	0	0	0
primaryKey.IdMapBase	0.000	0.000	0.001
primaryKey.Mixture	0	0	0
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.168	0.000	0.168
secondaryKey.CorrData	0	0	0
secondaryKey.IdMapBase	0.000	0.000	0.001
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.012	0.000	0.014
subsetData.JointUniquePairs	0.008	0.000	0.007
subsetGroups.JointUniquePairs	0.656	0.000	0.656
summary.IdMapDiffCounts	0.344	0.000	0.343
swapKeys.IdMap	0.056	0.004	0.059
swapKeys.UniquePairs	0.012	0.000	0.012
textBoundingBox.Display	0	0	0
to.base.Misc	0.004	0.000	0.000
to.binary.logical.Misc	0	0	0
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.048	0.000	0.049
words.Misc	0.000	0.000	0.001
zoom.pars.Display	0	0	0