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BioC 2.13: CHECK report for IdMappingAnalysis on zin1

This page was generated on 2014-04-05 09:48:15 -0700 (Sat, 05 Apr 2014).

Package 365/750HostnameOS / ArchBUILDCHECKBUILD BIN
IdMappingAnalysis 1.6.0
Alex Lisovich , Roger Day
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/IdMappingAnalysis
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: IdMappingAnalysis
Version: 1.6.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.6.0.tar.gz
StartedAt: 2014-04-05 01:56:25 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:57:40 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 74.4 seconds
RetCode: 0
Status:  OK 
CheckDir: IdMappingAnalysis.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.6.0’
* 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 ... [5s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘R.oo’ ‘rChoiceDialogs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... NOTE
prepare_Rd: DataFilter.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Display.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Misc.Rd:41-42: Dropping empty section \arguments
* 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 files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.661  0.004   7.672
Bootstrap                     6.816  0.044   6.905
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

IdMappingAnalysis.Rcheck/00install.out:

* 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)

IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings:

nameusersystemelapsed
000-LB-.IdMapBase0.3040.0080.313
Bootstrap6.8160.0446.905
Corr0.4960.0000.494
CorrData0.1400.0000.139
CsvList.merge.Misc0.0040.0000.005
IdMap0.0080.0000.009
IdMapBase0.0000.0000.003
IdMapCounts0.3440.0040.348
IdMapDiff0.5120.0040.540
IdMapDiffCounts0.3280.0000.329
JointIdMap0.0720.0000.072
JointUniquePairs0.6760.0080.682
Mixture0.3760.0000.377
UniquePairs0.0080.0000.010
aligned.IdMapBase0.0160.0000.016
as.IdMap.UniquePairs0.0440.0000.043
as.MultiSet.CorrData0.7080.0240.732
as.UniquePairs.IdMap0.0240.0000.025
as.data.frame.IdMapBase0.0720.0000.072
as.data.frame.JointIdMap0.0640.0000.067
as.list.IdMap0.0160.0000.018
boxplot.JointUniquePairs0.0800.0000.078
byColNames.Subset0.0080.0000.012
byColumn.Subset0.0080.0000.011
byRow.Subset0.0120.0000.010
byRowNames.Subset0.0120.0000.011
clust.Mixture0.0040.0000.006
copy.Display0.0040.0000.005
corr.boxplot.JointUniquePairs0.0800.0080.086
corr.plot.JointUniquePairs0.0560.0000.058
create.Display0.0040.0000.002
create.UniquePairs0.1160.0000.116
diffCounts.plot.JointIdMap0.4880.0000.490
dim.IdMapBase0.0120.0000.012
dimnames.IdMapBase0.0840.0000.083
do.glm.JointUniquePairs0.0240.0000.023
ecdf.plot.JointIdMap0.2080.0040.213
equals.UniquePairs0.0440.0000.043
fisherTransform.DataFilter0.0680.0000.068
fisherTransformInverse.DataFilter0.0000.0000.001
fisherTransformJacobean.DataFilter0.0000.0000.002
getBootstrap.JointUniquePairs7.6610.0047.672
getCompoundEvents.IdMapDiffCounts0.3720.0000.372
getCompoundGroups.IdMapDiffCounts0.3880.0000.390
getCorr.JointUniquePairs0.0680.0000.070
getCorrData.JointUniquePairs0.1560.0000.153
getCorrDataFrame.JointUniquePairs0.0320.0000.032
getCounts.IdMap0.0280.0000.029
getCounts.JointIdMap0.1840.0000.186
getData.Corr0.0040.0000.003
getData.Mixture0.0040.0000.004
getDiff.JointIdMap0.2080.0000.211
getExperimentSet.CorrData0.1080.0040.113
getIdMapList.JointIdMap0.0760.0000.074
getMapNames.JointIdMap0.1360.0000.137
getMapNames.JointUniquePairs0.0080.0000.006
getMatch.UniquePairs0.0480.0000.048
getMatchInfo.JointIdMap0.0720.0000.074
getMatchInfo.JointUniquePairs0.4080.0000.410
getMixture.JointUniquePairs0.2200.0000.222
getSampleNames.CorrData0.0080.0000.005
getStats.IdMapCounts0.1920.0040.199
getStats.Mixture0.0080.0000.007
getUnionIdMap.JointIdMap0.4640.0000.510
getUniquePairs.Corr0.0080.0000.010
getUniquePairs.CorrData0.0080.0000.008
getUniquePairs.JointUniquePairs0.0120.0000.010
interactive.corr.boxplot.JointUniquePairs0.1080.0000.224
interactive.corr.plot.JointUniquePairs0.0600.0040.065
interactive.mixture.boxplot.JointUniquePairs0.3000.0040.303
interactive.mixture.plot.JointUniquePairs0.2480.0000.251
interactive.plot.CorrData0.0560.0000.054
interactive.plot.JointUniquePairs0.0040.0000.006
interleave.Misc0.0040.0000.003
line.loess.Display0.0040.0000.004
line.unsorted.Display0.0040.0000.004
logTen.DataFilter0.2040.0000.204
merge.IdMap0.6280.0000.630
minAvgCountConstraint.DataFilter0.1400.0000.138
minCountConstraint.DataFilter0.1520.0040.154
minCountGroupConstraint.DataFilter0.2560.0000.259
mixture.boxplot.JointUniquePairs0.2920.0000.292
mixture.plot.JointUniquePairs0.2360.0000.237
plot.Bootstrap0.0800.0000.079
plot.Corr0.0640.0000.064
plot.CorrData0.0360.0000.035
plot.IdMapCounts0.1760.0000.177
plot.IdMapDiffCounts0.5760.0000.577
plot.Mixture0.0280.0000.028
primaryIDs.IdMapBase0.0200.0000.021
primaryKey.CorrData0.0040.0000.005
primaryKey.IdMapBase0.0040.0000.003
primaryKey.Mixture0.0040.0000.003
progressMsg.Display0.0040.0000.004
removeNASeries.DataFilter0.1560.0000.156
secondaryKey.CorrData0.0040.0000.005
secondaryKey.IdMapBase0.0040.0000.006
secondaryKey.Mixture0.0040.0000.003
subsetCorr.JointUniquePairs0.0200.0000.021
subsetData.JointUniquePairs0.0160.0000.018
subsetGroups.JointUniquePairs0.6200.0000.622
summary.IdMapDiffCounts0.4240.0000.425
swapKeys.IdMap0.060.000.06
swapKeys.UniquePairs0.0240.0000.022
textBoundingBox.Display0.0000.0000.001
to.base.Misc0.0000.0000.002
to.binary.logical.Misc0.0040.0000.005
to.index.expr.Misc0.0000.0000.004
unique.UniquePairs0.0640.0000.061
words.Misc0.0040.0000.004
zoom.pars.Display0.0040.0000.003