BioC 2.12: CHECK report for RNAither on lamb2

Package: RNAither

Version: 2.7.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.7.0.tar.gz

StartedAt: 2013-01-16 06:00:34 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:06:10 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 336.2 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.7.0’
* 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 ‘RNAither’ can be installed ... 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 33.386  0.836  36.393
rnaither     10.349  0.148  10.526
gseaAnalysis  6.017  0.060   8.464
* 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/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck/00check.log’
for details.

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘vignetteRNAither.Rnw’ 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (RNAither)

name	user	system	elapsed
BScore	0.084	0.000	0.084
DRQualControl	0.048	0.004	0.052
LiWongRank	0.108	0.008	0.118
MannWhitney	0.084	0.000	0.082
RankProduct	0.516	0.004	0.523
SNRQualControl	0.060	0.000	0.061
Ttest	0.060	0.012	0.069
ZPRIMEQualControl	0.084	0.004	0.089
ZScore	0.048	0.004	0.049
ZScorePerScreen	0.024	0.008	0.033
ZScorePlot	0.076	0.008	0.086
ZScorePlotTwo	0.428	0.000	0.426
channelPlot	0.052	0.008	0.062
closestToZero	0.016	0.004	0.024
compareHits	0.112	0.000	0.113
compareReplicaPlates	0.044	0.004	0.046
compareReplicateSD	0.216	0.004	0.220
compareReplicateSDPerScreen	0.296	0.016	0.315
compareReplicates	0.156	0.004	0.161
controlDensity	0.088	0.004	0.092
controlDensityPerPlate	0.200	0.004	0.203
controlDensityPerScreen	0.108	0.004	0.109
controlNorm	0.036	0.000	0.038
createSubset	0.028	0.000	0.027
discardLabtek	0.024	0.000	0.026
discardWells	0.024	0.004	0.026
divNorm	0.040	0.004	0.044
divideChannels	0.024	0.000	0.022
eraseDataSetColumn	0.032	0.000	0.036
findReplicates	0.028	0.000	0.028
furthestFromZero	0.016	0.000	0.016
generateDatasetFile	0.084	0.000	0.082
generateRepMatNoFilter	0.024	0.004	0.028
generateReplicateMat	0.032	0.000	0.032
gseaAnalysis	6.017	0.060	8.464
hitselectionPval	0.056	0.004	0.062
hitselectionZscore	0.060	0.004	0.072
hitselectionZscorePval	0.076	0.012	0.086
incorporatepValVec	0.048	0.012	0.057
indexSubset	0.02	0.00	0.02
joinDatasetFiles	0.056	0.008	0.066
joinDatasets	0.020	0.004	0.024
lowessNorm	0.044	0.000	0.044
mainAnalysis	33.386	0.836	36.393
makeBoxplot4PlateType	0.080	0.000	0.087
makeBoxplotControls	0.064	0.004	0.068
makeBoxplotControlsPerPlate	0.144	0.004	0.147
makeBoxplotControlsPerScreen	0.088	0.000	0.118
makeBoxplotPerPlate	0.096	0.004	0.099
makeBoxplotPerScreen	0.060	0.004	0.065
multTestAdjust	0.028	0.000	0.030
numCellQualControl	0.036	0.008	0.046
orderGeneIDs	0.068	0.000	0.068
percCellQualControl	0.044	0.000	0.044
plotBar	0.112	0.004	0.119
plotControlHisto	0.076	0.000	0.076
plotControlHistoPerplate	0.268	0.004	0.273
plotControlHistoPerscreen	0.144	0.008	0.148
plotHisto	0.036	0.000	0.035
plotHistoPerplate	0.076	0.008	0.083
plotHistoPerscreen	0.052	0.000	0.052
plotQQ	0.036	0.004	0.039
plotQQperplate	0.088	0.004	0.092
plotQQperscreen	0.056	0.004	0.060
quantileNormalization	0.040	0.004	0.047
replicatesCV	0.064	0.000	0.063
replicatesSpearmancor	0.032	0.008	0.039
rms	0.024	0.000	0.022
rnaither	10.349	0.148	10.526
saveDataset	0.036	0.004	0.040
saveOldIntensityColumns	0.016	0.000	0.020
savepValVec	0.02	0.00	0.02
spatialDistrib	0.592	0.000	0.590
spatialDistribHits	0.644	0.000	0.643
subtractBackground	0.016	0.008	0.028
sumChannels	0.044	0.004	0.045
summarizeReps	0.092	0.000	0.098
summarizeRepsNoFiltering	0.108	0.000	0.109
trim	0.036	0.000	0.034
varAdjust	0.032	0.004	0.035
vennDiag	0.160	0.008	0.168
volcanoPlot	0.108	0.000	0.110

Summary

Command output