Package: RNAither

Version: 2.1.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.1.0.tar.gz

StartedAt: 2011-05-09 14:01:16 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:05:32 -0700 (Mon, 09 May 2011)

EllapsedTime: 255.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘2.1.0’
* 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 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 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	0.056	0.000	0.056
DRQualControl	0.072	0.000	0.071
LiWongRank	0.124	0.004	0.131
MannWhitney	0.068	0.000	0.068
RankProduct	0.868	0.016	0.884
SNRQualControl	0.044	0.000	0.043
Ttest	0.048	0.000	0.049
ZPRIMEQualControl	0.060	0.008	0.120
ZScore	0.028	0.000	0.028
ZScorePerScreen	0.016	0.000	0.016
ZScorePlot	0.068	0.000	0.069
ZScorePlotTwo	0.036	0.000	0.033
channelPlot	0.032	0.008	0.039
closestToZero	0.004	0.000	0.006
compareHits	0.088	0.000	0.094
compareReplicaPlates	0.032	0.000	0.033
compareReplicateSD	0.244	0.000	0.243
compareReplicateSDPerScreen	0.296	0.000	0.299
compareReplicates	0.136	0.000	0.137
controlDensity	0.056	0.008	0.064
controlDensityPerPlate	0.188	0.000	0.188
controlDensityPerScreen	0.084	0.004	0.087
controlNorm	0.016	0.000	0.020
createSubset	0.008	0.000	0.006
discardLabtek	0.004	0.000	0.006
discardWells	0.008	0.000	0.010
divNorm	0.020	0.008	0.027
divideChannels	0.000	0.004	0.005
eraseDataSetColumn	0.012	0.000	0.015
findReplicates	0.012	0.000	0.009
furthestFromZero	0.004	0.000	0.005
generateDatasetFile	0.016	0.000	0.019
generateRepMatNoFilter	0.012	0.000	0.010
generateReplicateMat	0.012	0.000	0.014
gseaAnalysis	3.860	0.052	17.693
hitselectionPval	0.052	0.000	0.055
hitselectionZscore	0.040	0.000	0.042
hitselectionZscorePval	0.052	0.000	0.051
incorporatepValVec	0.028	0.004	0.033
indexSubset	0.008	0.000	0.005
joinDatasetFiles	0.024	0.004	0.031
joinDatasets	0.004	0.000	0.007
lowessNorm	0.016	0.000	0.019
mainAnalysis	32.118	0.484	34.549
makeBoxplot4PlateType	0.052	0.000	0.057
makeBoxplotControls	0.032	0.004	0.034
makeBoxplotControlsPerPlate	0.108	0.004	0.113
makeBoxplotControlsPerScreen	0.056	0.004	0.061
makeBoxplotPerPlate	0.068	0.000	0.546
makeBoxplotPerScreen	0.036	0.008	0.043
multTestAdjust	0.008	0.000	0.008
numCellQualControl	0.052	0.008	0.059
orderGeneIDs	0.128	0.000	0.133
percCellQualControl	0.052	0.000	0.049
plotBar	0.184	0.000	0.184
plotControlHisto	0.080	0.004	0.084
plotControlHistoPerplate	0.352	0.004	0.355
plotControlHistoPerscreen	0.172	0.000	0.173
plotHisto	0.024	0.004	0.028
plotHistoPerplate	0.081	0.004	0.086
plotHistoPerscreen	0.044	0.000	0.046
plotQQ	0.024	0.004	0.031
plotQQperplate	0.076	0.000	0.082
plotQQperscreen	0.044	0.008	0.049
quantileNormalization	0.032	0.000	0.034
replicatesCV	0.052	0.004	0.057
replicatesSpearmancor	0.036	0.000	0.037
rms	0.004	0.004	0.007
rnaither	11.760	0.128	11.928
saveDataset	0.020	0.004	0.026
saveOldIntensityColumns	0.008	0.000	0.008
savepValVec	0.004	0.004	0.007
spatialDistrib	0.524	0.008	0.532
spatialDistribHits	0.564	0.008	0.571
subtractBackground	0.020	0.004	0.021
sumChannels	0.024	0.004	0.027
summarizeReps	0.076	0.004	0.080
summarizeRepsNoFiltering	0.096	0.004	0.098
trim	0.008	0.004	0.013
varAdjust	0.016	0.000	0.018
vennDiag	0.104	0.008	0.113
volcanoPlot	0.064	0.004	0.070