Package: RNAither

Version: 2.1.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings RNAither_2.1.0.tar.gz

StartedAt: 2011-05-09 19:34:30 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 19:39:49 -0700 (Mon, 09 May 2011)

EllapsedTime: 318.9 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/RNAither.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.1.0'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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 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
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 (0.89) 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 1.3-00)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'vignetteRNAither.Rnw' 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-00)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.07	0.00	0.06
DRQualControl	0.11	0.00	0.11
LiWongRank	0.12	0.00	0.12
MannWhitney	0.05	0.00	0.05
RankProduct	0.78	0.00	0.78
SNRQualControl	0.03	0.02	0.05
Ttest	0.03	0.02	0.05
ZPRIMEQualControl	0.05	0.00	0.04
ZScore	0.01	0.00	0.02
ZScorePerScreen	0.02	0.00	0.02
ZScorePlot	0.03	0.03	0.06
ZScorePlotTwo	0.03	0.00	0.03
channelPlot	0.03	0.00	0.03
closestToZero	0	0	0
compareHits	0.08	0.00	0.10
compareReplicaPlates	0.03	0.00	0.03
compareReplicateSD	0.15	0.04	0.20
compareReplicateSDPerScreen	0.25	0.03	0.28
compareReplicates	0.11	0.02	0.13
controlDensity	0.05	0.02	0.06
controlDensityPerPlate	0.16	0.03	0.19
controlDensityPerScreen	0.06	0.01	0.08
controlNorm	0.02	0.02	0.03
createSubset	0	0	0
discardLabtek	0	0	0
discardWells	0.02	0.00	0.02
divNorm	0.01	0.00	0.02
divideChannels	0.02	0.00	0.01
eraseDataSetColumn	0.01	0.00	0.02
findReplicates	0.02	0.00	0.01
furthestFromZero	0	0	0
generateDatasetFile	0.01	0.00	0.02
generateRepMatNoFilter	0.02	0.00	0.01
generateReplicateMat	0.02	0.00	0.02
gseaAnalysis	3.96	0.15	21.87
hitselectionPval	0.05	0.02	0.07
hitselectionZscore	0.05	0.00	0.04
hitselectionZscorePval	0.05	0.00	0.05
incorporatepValVec	0.03	0.02	0.05
indexSubset	0	0	0
joinDatasetFiles	0.03	0.00	0.03
joinDatasets	0.01	0.00	0.01
lowessNorm	0.02	0.00	0.02
mainAnalysis	30.7	3.0	39.5
makeBoxplot4PlateType	0.05	0.01	0.06
makeBoxplotControls	0.19	0.02	0.22
makeBoxplotControlsPerPlate	0.09	0.01	0.11
makeBoxplotControlsPerScreen	0.03	0.03	0.06
makeBoxplotPerPlate	0.05	0.02	0.07
makeBoxplotPerScreen	0.03	0.00	0.03
multTestAdjust	0.02	0.00	0.01
numCellQualControl	0.04	0.00	0.05
orderGeneIDs	0.10	0.00	0.09
percCellQualControl	0.04	0.00	0.05
plotBar	0.13	0.05	0.17
plotControlHisto	0.11	0.00	0.11
plotControlHistoPerplate	0.39	0.04	0.44
plotControlHistoPerscreen	0.19	0.02	0.20
plotHisto	0.03	0.00	0.03
plotHistoPerplate	0.07	0.01	0.10
plotHistoPerscreen	0.04	0.02	0.04
plotQQ	0.01	0.02	0.03
plotQQperplate	0.03	0.04	0.08
plotQQperscreen	0.05	0.00	0.05
quantileNormalization	0.05	0.00	0.05
replicatesCV	0.04	0.00	0.04
replicatesSpearmancor	0.03	0.00	0.03
rms	0.02	0.00	0.02
rnaither	14.23	3.08	18.45
saveDataset	0.02	0.01	0.03
saveOldIntensityColumns	0.02	0.00	0.02
savepValVec	0.01	0.00	0.01
spatialDistrib	0.49	0.06	0.55
spatialDistribHits	0.60	0.04	0.63
subtractBackground	0.01	0.00	0.01
sumChannels	0.03	0.00	0.04
summarizeReps	0.10	0.00	0.09
summarizeRepsNoFiltering	0.07	0.00	0.08
trim	0	0	0
varAdjust	0.00	0.01	0.01
vennDiag	0.09	0.03	0.13
volcanoPlot	0.06	0.00	0.08