Package: RNAither

Version: 2.2.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch RNAither_2.2.0.tar.gz

StartedAt: 2012-01-09 05:24:16 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 05:30:19 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 362.5 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 2.14.1 (2011-12-22)
* 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 '2.2.0'
* 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 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 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                        old_size new_size compress
  datasetDrosophila.rda    763Kb    503Kb       xz
* 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
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "connection" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class "file" in package 'IRanges' seems equivalent to one from package 'graph' and is not turning on duplicate class definitions for this class

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

* DONE (RNAither)

name	user	system	elapsed
BScore	0.06	0.00	0.06
DRQualControl	0.11	0.00	0.11
LiWongRank	0.09	0.02	0.56
MannWhitney	0.03	0.00	0.03
RankProduct	0.75	0.01	0.76
SNRQualControl	0.06	0.00	0.18
Ttest	0.03	0.00	0.03
ZPRIMEQualControl	0.03	0.00	0.03
ZScore	0.01	0.00	0.02
ZScorePerScreen	0.04	0.00	0.03
ZScorePlot	0.06	0.00	0.06
ZScorePlotTwo	0.03	0.00	0.03
channelPlot	0.02	0.02	0.04
closestToZero	0	0	0
compareHits	0.08	0.00	0.08
compareReplicaPlates	0.01	0.00	0.06
compareReplicateSD	0.11	0.08	0.19
compareReplicateSDPerScreen	0.25	0.00	0.25
compareReplicates	0.07	0.07	0.14
controlDensity	0.03	0.02	0.05
controlDensityPerPlate	0.11	0.09	0.20
controlDensityPerScreen	0.08	0.00	0.08
controlNorm	0.03	0.00	0.03
createSubset	0	0	0
discardLabtek	0.01	0.00	0.01
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	0.00	0.02	0.01
furthestFromZero	0	0	0
generateDatasetFile	0.02	0.00	0.02
generateRepMatNoFilter	0.02	0.00	0.01
generateReplicateMat	0.01	0.00	0.02
gseaAnalysis	4.58	0.12	70.41
hitselectionPval	0.03	0.00	0.03
hitselectionZscore	0.05	0.00	0.04
hitselectionZscorePval	0.03	0.00	0.04
incorporatepValVec	0.01	0.04	0.04
indexSubset	0	0	0
joinDatasetFiles	0.02	0.00	0.03
joinDatasets	0.01	0.00	0.01
lowessNorm	0.02	0.00	0.02
mainAnalysis	27.68	3.70	37.38
makeBoxplot4PlateType	0.07	0.00	0.06
makeBoxplotControls	0.04	0.00	0.04
makeBoxplotControlsPerPlate	0.11	0.00	0.13
makeBoxplotControlsPerScreen	0.07	0.00	0.06
makeBoxplotPerPlate	0.01	0.03	0.05
makeBoxplotPerScreen	0.05	0.00	0.05
multTestAdjust	0	0	0
numCellQualControl	0.01	0.02	0.04
orderGeneIDs	0.07	0.01	0.08
percCellQualControl	0.04	0.00	0.05
plotBar	0.13	0.02	0.14
plotControlHisto	0.08	0.00	0.08
plotControlHistoPerplate	0.28	0.04	0.32
plotControlHistoPerscreen	0.15	0.02	0.18
plotHisto	0.02	0.01	0.03
plotHistoPerplate	0.06	0.02	0.08
plotHistoPerscreen	0.03	0.02	0.04
plotQQ	0.00	0.03	0.03
plotQQperplate	0.08	0.00	0.08
plotQQperscreen	0.03	0.01	0.05
quantileNormalization	0.03	0.00	0.03
replicatesCV	0.05	0.00	0.04
replicatesSpearmancor	0.04	0.00	0.05
rms	0	0	0
rnaither	11.88	3.30	17.25
saveDataset	0.03	0.00	0.03
saveOldIntensityColumns	0.02	0.00	0.02
savepValVec	0	0	0
spatialDistrib	0.46	0.09	0.56
spatialDistribHits	0.46	0.14	0.67
subtractBackground	0.00	0.02	0.02
sumChannels	0.01	0.02	0.03
summarizeReps	0.08	0.00	0.08
summarizeRepsNoFiltering	0.09	0.00	0.09
trim	0.02	0.00	0.02
varAdjust	0.02	0.00	0.01
vennDiag	0.07	0.04	0.13
volcanoPlot	0.07	0.00	0.06