Package: RNAither

Version: 1.99.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_1.99.0.tar.gz

StartedAt: 2011-02-24 16:46:32 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:50:38 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 246.2 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RNAither.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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	0.057	0.003	0.061
DRQualControl	0.183	0.004	0.187
LiWongRank	0.123	0.003	0.127
MannWhitney	0.052	0.002	0.054
RankProduct	0.658	0.006	0.663
SNRQualControl	0.038	0.005	0.043
Ttest	0.048	0.002	0.050
ZPRIMEQualControl	0.056	0.011	0.073
ZScore	0.024	0.001	0.024
ZScorePerScreen	0.013	0.002	0.015
ZScorePlot	0.151	0.019	0.186
ZScorePlotTwo	0.039	0.005	0.045
channelPlot	0.049	0.005	0.055
closestToZero	0.004	0.001	0.005
compareHits	0.089	0.006	0.094
compareReplicaPlates	0.026	0.002	0.028
compareReplicateSD	0.364	0.012	0.386
compareReplicateSDPerScreen	0.381	0.020	0.418
compareReplicates	0.271	0.033	0.354
controlDensity	0.075	0.008	0.089
controlDensityPerPlate	0.269	0.023	0.314
controlDensityPerScreen	0.133	0.015	0.162
controlNorm	0.021	0.001	0.022
createSubset	0.005	0.001	0.005
discardLabtek	0.009	0.001	0.009
discardWells	0.006	0.001	0.007
divNorm	0.020	0.002	0.022
divideChannels	0.004	0.001	0.005
eraseDataSetColumn	0.015	0.002	0.018
findReplicates	0.007	0.001	0.009
furthestFromZero	0.004	0.000	0.005
generateDatasetFile	0.014	0.001	0.024
generateRepMatNoFilter	0.010	0.001	0.011
generateReplicateMat	0.014	0.001	0.016
gseaAnalysis	3.289	0.041	20.958
hitselectionPval	0.050	0.002	0.052
hitselectionZscore	0.054	0.003	0.057
hitselectionZscorePval	0.052	0.003	0.055
incorporatepValVec	0.037	0.002	0.040
indexSubset	0.004	0.000	0.006
joinDatasetFiles	0.026	0.003	0.030
joinDatasets	0.006	0.001	0.007
lowessNorm	0.025	0.002	0.027
mainAnalysis	43.675	3.234	51.087
makeBoxplot4PlateType	0.081	0.008	0.096
makeBoxplotControls	0.046	0.005	0.054
makeBoxplotControlsPerPlate	0.175	0.014	0.205
makeBoxplotControlsPerScreen	0.087	0.008	0.104
makeBoxplotPerPlate	0.083	0.008	0.096
makeBoxplotPerScreen	0.045	0.005	0.052
multTestAdjust	0.004	0.001	0.005
numCellQualControl	0.039	0.004	0.042
orderGeneIDs	0.109	0.002	0.111
percCellQualControl	0.036	0.004	0.041
plotBar	0.337	0.011	0.358
plotControlHisto	0.119	0.007	0.131
plotControlHistoPerplate	0.504	0.020	0.549
plotControlHistoPerscreen	0.252	0.010	0.274
plotHisto	0.039	0.006	0.048
plotHistoPerplate	0.157	0.017	0.189
plotHistoPerscreen	0.076	0.009	0.091
plotQQ	0.042	0.006	0.052
plotQQperplate	0.152	0.016	0.180
plotQQperscreen	0.078	0.009	0.091
quantileNormalization	0.034	0.003	0.037
replicatesCV	0.089	0.009	0.103
replicatesSpearmancor	0.032	0.004	0.036
rms	0.004	0.001	0.005
rnaither	19.023	0.365	19.526
saveDataset	0.032	0.003	0.035
saveOldIntensityColumns	0.006	0.001	0.007
savepValVec	0.006	0.001	0.007
spatialDistrib	0.832	0.045	0.919
spatialDistribHits	0.904	0.046	0.991
subtractBackground	0.010	0.002	0.012
sumChannels	0.022	0.002	0.024
summarizeReps	0.096	0.002	0.097
summarizeRepsNoFiltering	0.103	0.002	0.105
trim	0.009	0.003	0.010
varAdjust	0.014	0.002	0.016
vennDiag	0.143	0.011	0.159
volcanoPlot	0.094	0.008	0.103