Package: RNAither

Version: 2.0.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.0.0.tar.gz

StartedAt: 2011-10-20 14:17:13 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:21:55 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 282.1 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/RNAither.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘2.0.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RNAither’ 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 ... NOTE
Found the following CITATION file(s) 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 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 ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.052	0.004	0.057
DRQualControl	0.300	0.000	0.301
LiWongRank	0.124	0.008	0.135
MannWhitney	0.064	0.000	0.066
RankProduct	0.656	0.000	0.655
SNRQualControl	0.032	0.004	0.037
Ttest	0.048	0.008	0.055
ZPRIMEQualControl	0.076	0.016	0.095
ZScore	0.016	0.008	0.023
ZScorePerScreen	0.020	0.000	0.017
ZScorePlot	0.092	0.008	0.097
ZScorePlotTwo	0.036	0.000	0.036
channelPlot	0.048	0.008	0.054
closestToZero	0.008	0.000	0.008
compareHits	0.084	0.004	0.090
compareReplicaPlates	0.024	0.004	0.028
compareReplicateSD	0.228	0.004	0.231
compareReplicateSDPerScreen	0.292	0.004	0.296
compareReplicates	0.140	0.000	0.139
controlDensity	0.080	0.004	0.081
controlDensityPerPlate	0.176	0.000	0.181
controlDensityPerScreen	0.080	0.000	0.083
controlNorm	0.024	0.000	0.024
createSubset	0.004	0.004	0.005
discardLabtek	0.008	0.000	0.005
discardWells	0.004	0.000	0.007
divNorm	0.016	0.000	0.017
divideChannels	0.004	0.000	0.005
eraseDataSetColumn	0.016	0.000	0.015
findReplicates	0.008	0.004	0.009
furthestFromZero	0.004	0.000	0.005
generateDatasetFile	0.012	0.000	0.013
generateRepMatNoFilter	0.008	0.000	0.010
generateReplicateMat	0.012	0.004	0.014
gseaAnalysis	5.184	0.060	39.195
hitselectionPval	0.036	0.004	0.039
hitselectionZscore	0.036	0.000	0.043
hitselectionZscorePval	0.052	0.000	0.052
incorporatepValVec	0.028	0.004	0.035
indexSubset	0.004	0.000	0.006
joinDatasetFiles	0.028	0.000	0.028
joinDatasets	0.008	0.000	0.008
lowessNorm	0.024	0.000	0.021
mainAnalysis	36.091	0.596	39.286
makeBoxplot4PlateType	0.052	0.008	0.062
makeBoxplotControls	0.028	0.012	0.040
makeBoxplotControlsPerPlate	0.120	0.004	0.124
makeBoxplotControlsPerScreen	0.072	0.000	0.075
makeBoxplotPerPlate	0.060	0.004	0.065
makeBoxplotPerScreen	0.044	0.000	0.042
multTestAdjust	0.004	0.004	0.007
numCellQualControl	0.044	0.000	0.041
orderGeneIDs	0.096	0.008	0.104
percCellQualControl	0.036	0.008	0.042
plotBar	0.140	0.008	0.151
plotControlHisto	0.088	0.004	0.091
plotControlHistoPerplate	0.380	0.000	0.378
plotControlHistoPerscreen	0.184	0.004	0.188
plotHisto	0.028	0.000	0.027
plotHistoPerplate	0.092	0.000	0.093
plotHistoPerscreen	0.044	0.000	0.046
plotQQ	0.036	0.000	0.036
plotQQperplate	0.1	0.0	0.1
plotQQperscreen	0.056	0.004	0.059
quantileNormalization	0.036	0.000	0.036
replicatesCV	0.056	0.004	0.059
replicatesSpearmancor	0.032	0.000	0.031
rms	0.008	0.000	0.006
rnaither	14.637	0.112	14.760
saveDataset	0.028	0.000	0.029
saveOldIntensityColumns	0.008	0.000	0.008
savepValVec	0.004	0.004	0.008
spatialDistrib	0.636	0.008	0.647
spatialDistribHits	0.672	0.008	0.682
subtractBackground	0.012	0.004	0.014
sumChannels	0.024	0.004	0.027
summarizeReps	0.096	0.000	0.098
summarizeRepsNoFiltering	0.080	0.004	0.085
trim	0.012	0.004	0.013
varAdjust	0.020	0.000	0.019
vennDiag	0.136	0.012	0.150
volcanoPlot	0.068	0.008	0.077