Package: IdMappingAnalysis

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.0.1.tar.gz

StartedAt: 2012-09-24 00:37:28 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:39:26 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 118.1 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.0.1'
* 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
** 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	0.495	0.058	0.553
Bootstrap	8.563	0.032	8.591
Corr	0.599	0.011	0.610
CorrData	0.161	0.016	0.177
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.005	0.001	0.006
IdMapBase	0.001	0.000	0.001
IdMapCounts	0.732	0.018	0.750
IdMapDiff	0.778	0.015	0.795
IdMapDiffCounts	0.570	0.011	0.580
JointIdMap	0.208	0.005	0.214
JointUniquePairs	1.400	0.040	1.441
Mixture	0.375	0.010	0.406
UniquePairs	0.003	0.001	0.003
aligned.IdMapBase	0.010	0.001	0.010
as.IdMap.UniquePairs	0.097	0.004	0.101
as.MultiSet.CorrData	1.119	0.040	1.161
as.UniquePairs.IdMap	0.037	0.003	0.040
as.data.frame.IdMapBase	0.152	0.030	0.183
as.data.frame.JointIdMap	0.302	0.007	0.308
as.list.IdMap	0.021	0.003	0.024
boxplot.JointUniquePairs	0.079	0.003	0.082
byColNames.Subset	0.007	0.000	0.007
byColumn.Subset	0.012	0.000	0.013
byRow.Subset	0.017	0.008	0.026
byRowNames.Subset	0.012	0.001	0.012
clust.Mixture	0.001	0.000	0.001
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.106	0.005	0.112
corr.plot.JointUniquePairs	0.079	0.008	0.091
create.Display	0.000	0.000	0.001
create.UniquePairs	0.152	0.017	0.173
diffCounts.plot.JointIdMap	0.896	0.016	0.912
dim.IdMapBase	0.009	0.008	0.016
dimnames.IdMapBase	0.013	0.003	0.016
do.glm.JointUniquePairs	0.023	0.002	0.026
ecdf.plot.JointIdMap	0.367	0.009	0.376
equals.UniquePairs	0.044	0.003	0.047
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0.001	0.000	0.000
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	8.739	0.036	8.816
getCompoundEvents.IdMapDiffCounts	0.827	0.018	0.845
getCompoundGroups.IdMapDiffCounts	0.612	0.014	0.628
getCorr.JointUniquePairs	0.095	0.010	0.106
getCorrData.JointUniquePairs	0.363	0.024	0.386
getCorrDataFrame.JointUniquePairs	0.032	0.002	0.035
getCounts.IdMap	0.043	0.001	0.043
getCounts.JointIdMap	0.528	0.012	0.540
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.001	0.000	0.001
getDiff.JointIdMap	0.636	0.011	0.647
getExperimentSet.CorrData	0.212	0.016	0.227
getIdMapList.JointIdMap	0.39	0.01	0.40
getMapNames.JointIdMap	0.289	0.007	0.297
getMapNames.JointUniquePairs	0.001	0.001	0.002
getMatch.UniquePairs	0.065	0.005	0.070
getMatchInfo.JointIdMap	0.282	0.006	0.288
getMatchInfo.JointUniquePairs	0.635	0.004	0.639
getMixture.JointUniquePairs	0.202	0.008	0.210
getSampleNames.CorrData	0.001	0.001	0.001
getStats.IdMapCounts	0.358	0.014	0.373
getStats.Mixture	0.002	0.001	0.002
getUnionIdMap.JointIdMap	0.659	0.013	0.673
getUniquePairs.Corr	0.004	0.001	0.004
getUniquePairs.CorrData	0.004	0.001	0.005
getUniquePairs.JointUniquePairs	0.004	0.001	0.004
interactive.corr.boxplot.JointUniquePairs	0.077	0.004	0.082
interactive.corr.plot.JointUniquePairs	0.052	0.062	0.115
interactive.mixture.boxplot.JointUniquePairs	0.245	0.062	0.308
interactive.mixture.plot.JointUniquePairs	0.205	0.064	0.270
interactive.plot.CorrData	0.054	0.004	0.057
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	0.021	0.004	0.025
merge.IdMap	0.847	0.013	0.861
minAvgCountConstraint.DataFilter	0.223	0.043	0.265
minCountConstraint.DataFilter	0.236	0.065	0.305
minCountGroupConstraint.DataFilter	0.333	0.067	0.400
mixture.boxplot.JointUniquePairs	0.411	0.016	0.428
mixture.plot.JointUniquePairs	0.276	0.010	0.287
plot.Bootstrap	0.141	0.005	0.145
plot.Corr	0.092	0.009	0.101
plot.CorrData	0.050	0.002	0.052
plot.IdMapCounts	0.531	0.014	0.545
plot.IdMapDiffCounts	1.314	0.022	1.337
plot.Mixture	0.027	0.003	0.029
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0	0	0
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.349	0.072	0.420
secondaryKey.CorrData	0.001	0.000	0.000
secondaryKey.IdMapBase	0.002	0.000	0.003
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.023	0.002	0.025
subsetData.JointUniquePairs	0.010	0.000	0.011
subsetGroups.JointUniquePairs	1.325	0.046	1.372
summary.IdMapDiffCounts	0.892	0.018	0.909
swapKeys.IdMap	0.192	0.008	0.200
swapKeys.UniquePairs	0.040	0.004	0.044
textBoundingBox.Display	0	0	0
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0.000	0.001	0.000
unique.UniquePairs	0.103	0.014	0.118
words.Misc	0.001	0.000	0.000
zoom.pars.Display	0.000	0.000	0.001