Package: RNAither

Version: 1.8.1

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_1.8.1.tar.gz

StartedAt: 2010-10-04 19:35:39 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 19:38:58 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 198.7 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/RNAither.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '1.8.1'
* 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 ... OK
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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
  'openVignette()'. 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	0.260	0.008	0.269
DRQualControl	0.072	0.004	0.086
LiWongRank	0.164	0.004	0.167
MannWhitney	0.064	0.000	0.063
RankProduct	0.736	0.000	0.770
SNRQualControl	0.032	0.004	0.065
Ttest	0.060	0.004	0.062
ZPRIMEQualControl	0.076	0.004	0.091
ZScore	0.028	0.000	0.027
ZScorePerScreen	0.016	0.000	0.014
ZScorePlot	0.076	0.000	0.079
ZScorePlotTwo	0.032	0.000	0.033
channelPlot	0.048	0.004	0.051
closestToZero	0.000	0.004	0.004
compareHits	0.076	0.004	0.087
compareReplicaPlates	0.028	0.000	0.051
compareReplicateSD	0.480	0.012	0.493
compareReplicateSDPerScreen	0.304	0.012	0.318
compareReplicates	0.140	0.000	0.143
controlDensity	0.080	0.000	0.083
controlDensityPerPlate	0.188	0.000	0.187
controlDensityPerScreen	0.084	0.004	0.088
controlNorm	0.020	0.000	0.021
createSubset	0.004	0.000	0.005
discardLabtek	0.000	0.004	0.005
discardWells	0.004	0.000	0.006
divNorm	0.024	0.000	0.023
divideChannels	0.000	0.004	0.004
eraseDataSetColumn	0.020	0.000	0.021
findReplicates	0.004	0.004	0.006
furthestFromZero	0.000	0.004	0.004
generateDatasetFile	0.012	0.004	0.012
generateRepMatNoFilter	0.016	0.000	0.018
generateReplicateMat	0.024	0.000	0.024
gseaAnalysis	5.136	0.084	9.980
hitselectionPval	0.044	0.000	0.044
hitselectionZscore	0.036	0.004	0.043
hitselectionZscorePval	0.044	0.000	0.045
incorporatepValVec	0.048	0.000	0.047
indexSubset	0.004	0.000	0.005
joinDatasetFiles	0.020	0.000	0.022
joinDatasets	0.004	0.004	0.006
lowessNorm	0.016	0.004	0.019
mainAnalysis	36.867	0.432	42.016
makeBoxplot4PlateType	0.056	0.004	0.060
makeBoxplotControls	0.036	0.000	0.035
makeBoxplotControlsPerPlate	0.116	0.004	0.117
makeBoxplotControlsPerScreen	0.068	0.000	0.069
makeBoxplotPerPlate	0.056	0.004	0.059
makeBoxplotPerScreen	0.032	0.000	0.034
multTestAdjust	0.000	0.004	0.005
numCellQualControl	0.040	0.000	0.038
orderGeneIDs	0.128	0.004	0.133
percCellQualControl	0.024	0.012	0.036
plotBar	0.152	0.000	0.156
plotControlHisto	0.088	0.000	0.087
plotControlHistoPerplate	0.388	0.000	0.389
plotControlHistoPerscreen	0.196	0.000	0.196
plotHisto	0.020	0.004	0.023
plotHistoPerplate	0.076	0.012	0.086
plotHistoPerscreen	0.044	0.004	0.045
plotQQ	0.032	0.000	0.032
plotQQperplate	0.088	0.004	0.092
plotQQperscreen	0.052	0.000	0.054
quantileNormalization	0.036	0.000	0.035
replicatesCV	0.060	0.000	0.063
replicatesSpearmancor	0.040	0.000	0.042
rms	0.008	0.000	0.004
saveDataset	0.020	0.004	0.026
saveOldIntensityColumns	0.004	0.000	0.005
savepValVec	0.008	0.000	0.006
spatialDistrib	0.636	0.004	0.640
spatialDistribHits	0.668	0.012	0.678
subtractBackground	0.008	0.000	0.010
sumChannels	0.024	0.000	0.023
summarizeReps	0.116	0.000	0.115
summarizeRepsNoFiltering	0.112	0.000	0.111
trim	0.004	0.004	0.009
varAdjust	0.016	0.000	0.015
vennDiag	0.116	0.004	0.119
volcanoPlot	0.068	0.004	0.075