Package: RNAither

Version: 1.99.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_1.99.0.tar.gz

StartedAt: 2011-02-24 22:26:26 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 22:30:11 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 225.5 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 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘1.99.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘RNAither’ can be installed ... 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:
  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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: SparseM
Package SparseM (0.86) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RNAither)

name	user	system	elapsed
BScore	0.052	0.004	0.055
DRQualControl	0.280	0.008	0.285
LiWongRank	0.104	0.016	0.118
MannWhitney	0.048	0.000	0.049
RankProduct	0.604	0.004	0.607
SNRQualControl	0.04	0.00	0.04
Ttest	0.040	0.008	0.046
ZPRIMEQualControl	0.056	0.016	0.078
ZScore	0.016	0.008	0.021
ZScorePerScreen	0.016	0.000	0.015
ZScorePlot	0.072	0.004	0.074
ZScorePlotTwo	0.032	0.004	0.035
channelPlot	0.040	0.000	0.043
closestToZero	0.004	0.000	0.005
compareHits	0.072	0.016	0.088
compareReplicaPlates	0.028	0.004	0.029
compareReplicateSD	0.436	0.004	0.442
compareReplicateSDPerScreen	0.300	0.000	0.298
compareReplicates	0.128	0.008	0.137
controlDensity	0.068	0.004	0.070
controlDensityPerPlate	0.184	0.008	0.191
controlDensityPerScreen	0.076	0.008	0.102
controlNorm	0.024	0.000	0.027
createSubset	0.004	0.000	0.005
discardLabtek	0.004	0.004	0.006
discardWells	0.008	0.000	0.007
divNorm	0.012	0.008	0.021
divideChannels	0.004	0.000	0.005
eraseDataSetColumn	0.012	0.004	0.015
findReplicates	0.008	0.004	0.010
furthestFromZero	0.004	0.000	0.005
generateDatasetFile	0.012	0.000	0.013
generateRepMatNoFilter	0.012	0.000	0.010
generateReplicateMat	0.020	0.000	0.021
gseaAnalysis	4.040	0.028	16.366
hitselectionPval	0.032	0.008	0.038
hitselectionZscore	0.036	0.012	0.045
hitselectionZscorePval	0.048	0.000	0.050
incorporatepValVec	0.028	0.000	0.030
indexSubset	0.000	0.004	0.005
joinDatasetFiles	0.012	0.012	0.023
joinDatasets	0.008	0.000	0.006
lowessNorm	0.016	0.004	0.019
mainAnalysis	32.658	0.368	34.882
makeBoxplot4PlateType	0.056	0.008	0.061
makeBoxplotControls	0.044	0.000	0.045
makeBoxplotControlsPerPlate	0.116	0.004	0.120
makeBoxplotControlsPerScreen	0.068	0.000	0.066
makeBoxplotPerPlate	0.064	0.000	0.069
makeBoxplotPerScreen	0.032	0.004	0.036
multTestAdjust	0.008	0.000	0.006
numCellQualControl	0.040	0.000	0.042
orderGeneIDs	0.096	0.004	0.103
percCellQualControl	0.036	0.004	0.040
plotBar	0.152	0.008	0.160
plotControlHisto	0.1	0.0	0.1
plotControlHistoPerplate	0.364	0.000	0.370
plotControlHistoPerscreen	0.188	0.004	0.191
plotHisto	0.028	0.004	0.030
plotHistoPerplate	0.096	0.000	0.095
plotHistoPerscreen	0.044	0.004	0.048
plotQQ	0.024	0.008	0.036
plotQQperplate	0.088	0.004	0.094
plotQQperscreen	0.052	0.004	0.059
quantileNormalization	0.032	0.004	0.037
replicatesCV	0.064	0.000	0.061
replicatesSpearmancor	0.028	0.008	0.036
rms	0.004	0.000	0.007
rnaither	14.705	0.104	14.989
saveDataset	0.032	0.000	0.031
saveOldIntensityColumns	0.008	0.000	0.008
savepValVec	0.008	0.000	0.009
spatialDistrib	0.612	0.004	0.618
spatialDistribHits	0.664	0.004	0.676
subtractBackground	0.012	0.000	0.014
sumChannels	0.020	0.004	0.026
summarizeReps	0.088	0.004	0.090
summarizeRepsNoFiltering	0.096	0.004	0.102
trim	0.012	0.000	0.013
varAdjust	0.016	0.000	0.017
vennDiag	0.132	0.008	0.139
volcanoPlot	0.076	0.000	0.078