BioC 2.12: CHECK report for IdMappingAnalysis on petty

Package: IdMappingAnalysis

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.4.0.tar.gz

StartedAt: 2013-10-08 22:49:06 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:51:27 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 141.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: IdMappingAnalysis.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' version '1.4.0'
* 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 ... [12s/12s] 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NB: .First.lib is obsolete and will not be used in R 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 sizes of PDF files under 'inst/doc' ... 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	0.697	0.042	0.739
Bootstrap	13.690	0.313	14.122
Corr	0.926	0.039	0.976
CorrData	0.301	0.023	0.327
CsvList.merge.Misc	0.010	0.002	0.011
IdMap	0.025	0.001	0.030
IdMapBase	0.009	0.002	0.010
IdMapCounts	0.801	0.021	0.830
IdMapDiff	1.077	0.010	1.089
IdMapDiffCounts	0.681	0.011	0.721
JointIdMap	0.191	0.007	0.207
JointUniquePairs	1.151	0.014	1.175
Mixture	0.367	0.005	0.372
UniquePairs	0.012	0.005	0.018
aligned.IdMapBase	0.026	0.011	0.037
as.IdMap.UniquePairs	0.066	0.005	0.071
as.MultiSet.CorrData	1.344	0.053	1.410
as.UniquePairs.IdMap	0.047	0.008	0.056
as.data.frame.IdMapBase	0.160	0.005	0.167
as.data.frame.JointIdMap	0.161	0.003	0.192
as.list.IdMap	0.041	0.001	0.042
boxplot.JointUniquePairs	0.163	0.006	0.169
byColNames.Subset	0.124	0.006	0.131
byColumn.Subset	0.015	0.006	0.022
byRow.Subset	0.016	0.006	0.022
byRowNames.Subset	0.026	0.006	0.031
clust.Mixture	0.009	0.003	0.014
copy.Display	0.007	0.004	0.010
corr.boxplot.JointUniquePairs	0.166	0.008	0.177
corr.plot.JointUniquePairs	0.11	0.01	0.12
create.Display	0.008	0.004	0.011
create.UniquePairs	0.172	0.005	0.179
diffCounts.plot.JointIdMap	0.887	0.012	0.922
dim.IdMapBase	0.022	0.007	0.029
dimnames.IdMapBase	0.166	0.004	0.184
do.glm.JointUniquePairs	0.047	0.005	0.053
ecdf.plot.JointIdMap	0.402	0.015	0.419
equals.UniquePairs	0.061	0.006	0.078
fisherTransform.DataFilter	0.007	0.003	0.010
fisherTransformInverse.DataFilter	0.007	0.003	0.011
fisherTransformJacobean.DataFilter	0.007	0.003	0.011
getBootstrap.JointUniquePairs	14.510	0.328	15.054
getCompoundEvents.IdMapDiffCounts	0.670	0.010	0.685
getCompoundGroups.IdMapDiffCounts	0.721	0.020	0.745
getCorr.JointUniquePairs	0.121	0.005	0.127
getCorrData.JointUniquePairs	0.444	0.021	0.466
getCorrDataFrame.JointUniquePairs	0.049	0.006	0.054
getCounts.IdMap	0.040	0.005	0.045
getCounts.JointIdMap	0.328	0.013	0.351
getData.Corr	0.009	0.005	0.019
getData.Mixture	0.012	0.006	0.019
getDiff.JointIdMap	0.367	0.011	0.429
getExperimentSet.CorrData	0.226	0.022	0.252
getIdMapList.JointIdMap	0.177	0.006	0.190
getMapNames.JointIdMap	0.148	0.003	0.151
getMapNames.JointUniquePairs	0.006	0.004	0.009
getMatch.UniquePairs	0.070	0.008	0.078
getMatchInfo.JointIdMap	0.149	0.005	0.155
getMatchInfo.JointUniquePairs	0.777	0.006	0.788
getMixture.JointUniquePairs	0.282	0.007	0.290
getSampleNames.CorrData	0.010	0.004	0.015
getStats.IdMapCounts	0.358	0.009	0.376
getStats.Mixture	0.013	0.003	0.016
getUnionIdMap.JointIdMap	0.837	0.014	0.856
getUniquePairs.Corr	0.017	0.005	0.022
getUniquePairs.CorrData	0.018	0.004	0.022
getUniquePairs.JointUniquePairs	0.024	0.004	0.029
interactive.corr.boxplot.JointUniquePairs	0.170	0.009	0.180
interactive.corr.plot.JointUniquePairs	0.119	0.014	0.134
interactive.mixture.boxplot.JointUniquePairs	0.393	0.020	0.415
interactive.mixture.plot.JointUniquePairs	0.308	0.016	0.323
interactive.plot.CorrData	0.111	0.007	0.124
interactive.plot.JointUniquePairs	0.009	0.003	0.014
interleave.Misc	0.008	0.003	0.011
line.loess.Display	0.015	0.005	0.021
line.unsorted.Display	0.016	0.003	0.020