BioC 2.12: CHECK report for IdMappingAnalysis on george2

Package: IdMappingAnalysis

Version: 1.4.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.4.0.tar.gz

StartedAt: 2013-10-09 02:40:18 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:42:26 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 128.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: IdMappingAnalysis.Rcheck

Warnings: NA

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdMappingAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingAnalysis’ version ‘1.4.0’
* 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 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 ... [9s/10s] 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NB: .First.lib is obsolete and will not be used in R 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 installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘IdMappingAnalysis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: log10.DataFilter
> ### Title: Compute log10 of a numerical vector combined with thresholding
> ###   on minimum value
> ### Aliases: log10.DataFilter DataFilter.log10 log10.DataFilter
> ###   log10,DataFilter-method
> ### Keywords: internal methods
> 
> ### ** Examples
> 
>  #compute log10 transform of mrna experiment data replacing (clipping)
>  #the output values with log10(0.5)for input values < 0.5
>  fltExperimentSet<-DataFilter$do.apply(examples$mrnaExperimentSet,
+          byRows=TRUE,filterFun=DataFilter$log10,filtParams=c(0.5,log10(0.5)),verbose=TRUE);
filtering experiment set...
Error in log10(static, ...) : 
  3 arguments passed to 'log10' which requires 1
Calls: <Anonymous> -> do.apply -> do.apply.DataFilter -> filterFun
Execution halted

* 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
** testing if installed package can be loaded
* DONE (IdMappingAnalysis)

name	user	system	elapsed
000-LB-.IdMapBase	1.116	0.048	1.162
Bootstrap	12.929	0.040	12.985
Corr	0.836	0.008	0.845
CorrData	0.612	0.000	0.611
CsvList.merge.Misc	0.032	0.000	0.031
IdMap	0.040	0.000	0.038
IdMapBase	0.016	0.000	0.016
IdMapCounts	0.636	0.000	0.637
IdMapDiff	1.168	0.004	1.170
IdMapDiffCounts	0.896	0.008	0.901
JointIdMap	0.120	0.000	0.122
JointUniquePairs	1.120	0.000	1.268
Mixture	0.492	0.004	0.521
UniquePairs	0.060	0.000	0.059
aligned.IdMapBase	0.060	0.000	0.059
as.IdMap.UniquePairs	0.108	0.000	0.107
as.MultiSet.CorrData	1.628	0.032	1.665
as.UniquePairs.IdMap	0.060	0.004	0.063
as.data.frame.IdMapBase	0.168	0.000	0.169
as.data.frame.JointIdMap	0.144	0.000	0.142
as.list.IdMap	0.040	0.000	0.042
boxplot.JointUniquePairs	0.164	0.000	0.166
byColNames.Subset	0.236	0.000	0.237
byColumn.Subset	0.032	0.000	0.028
byRow.Subset	0.048	0.000	0.047
byRowNames.Subset	0.036	0.000	0.036
clust.Mixture	0.020	0.000	0.019
copy.Display	0.016	0.000	0.016
corr.boxplot.JointUniquePairs	0.176	0.000	0.176
corr.plot.JointUniquePairs	0.128	0.000	0.127
create.Display	0.012	0.000	0.013
create.UniquePairs	0.24	0.00	0.24
diffCounts.plot.JointIdMap	1.16	0.00	1.16
dim.IdMapBase	0.056	0.000	0.057
dimnames.IdMapBase	0.3	0.0	0.3
do.glm.JointUniquePairs	0.084	0.000	0.083
ecdf.plot.JointIdMap	0.484	0.000	0.481
equals.UniquePairs	0.096	0.004	0.099
fisherTransform.DataFilter	0.024	0.000	0.021
fisherTransformInverse.DataFilter	0.004	0.000	0.007
fisherTransformJacobean.DataFilter	0.004	0.000	0.007
getBootstrap.JointUniquePairs	13.537	0.020	13.885
getCompoundEvents.IdMapDiffCounts	0.636	0.008	0.645
getCompoundGroups.IdMapDiffCounts	0.74	0.00	0.74
getCorr.JointUniquePairs	0.132	0.008	0.140
getCorrData.JointUniquePairs	0.768	0.004	0.767
getCorrDataFrame.JointUniquePairs	0.048	0.004	0.053
getCounts.IdMap	0.048	0.000	0.048
getCounts.JointIdMap	0.312	0.000	0.312
getData.Corr	0.02	0.00	0.02
getData.Mixture	0.044	0.000	0.041
getDiff.JointIdMap	0.648	0.000	0.647
getExperimentSet.CorrData	0.276	0.000	0.277
getIdMapList.JointIdMap	0.156	0.000	0.155
getMapNames.JointIdMap	0.120	0.000	0.121
getMapNames.JointUniquePairs	0.016	0.000	0.015
getMatch.UniquePairs	0.088	0.004	0.093
getMatchInfo.JointIdMap	0.128	0.004	0.133
getMatchInfo.JointUniquePairs	0.692	0.000	0.697
getMixture.JointUniquePairs	0.364	0.000	0.363
getSampleNames.CorrData	0.028	0.000	0.024
getStats.IdMapCounts	0.393	0.004	0.396
getStats.Mixture	0.008	0.000	0.011
getUnionIdMap.JointIdMap	0.748	0.004	0.757
getUniquePairs.Corr	0.024	0.004	0.027
getUniquePairs.CorrData	0.028	0.000	0.029
getUniquePairs.JointUniquePairs	0.024	0.000	0.026
interactive.corr.boxplot.JointUniquePairs	0.144	0.004	0.147
interactive.corr.plot.JointUniquePairs	0.104	0.008	0.110
interactive.mixture.boxplot.JointUniquePairs	0.432	0.004	0.436
interactive.mixture.plot.JointUniquePairs	0.356	0.004	0.360
interactive.plot.CorrData	0.100	0.004	0.105
interactive.plot.JointUniquePairs	0.012	0.004	0.016
interleave.Misc	0.012	0.000	0.014
line.loess.Display	0.020	0.000	0.021
line.unsorted.Display	0.008	0.000	0.007