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 21:11:37 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:16:53 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 316.6 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: UTF-8
* 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	0.079	0.006	0.085
DRQualControl	0.256	0.006	0.263
LiWongRank	0.170	0.007	0.177
MannWhitney	0.074	0.004	0.080
RankProduct	0.895	0.007	0.906
SNRQualControl	0.055	0.007	0.069
Ttest	0.067	0.002	0.069
ZPRIMEQualControl	0.068	0.012	0.088
ZScore	0.033	0.003	0.036
ZScorePerScreen	0.020	0.003	0.024
ZScorePlot	0.158	0.008	0.171
ZScorePlotTwo	0.048	0.005	0.054
channelPlot	0.059	0.006	0.066
closestToZero	0.006	0.001	0.008
compareHits	0.116	0.006	0.121
compareReplicaPlates	0.035	0.004	0.039
compareReplicateSD	0.457	0.013	0.473
compareReplicateSDPerScreen	0.499	0.023	0.523
compareReplicates	0.280	0.013	0.295
controlDensity	0.087	0.008	0.095
controlDensityPerPlate	0.314	0.020	0.335
controlDensityPerScreen	0.145	0.011	0.156
controlNorm	0.028	0.003	0.032
createSubset	0.007	0.002	0.009
discardLabtek	0.013	0.002	0.014
discardWells	0.009	0.002	0.011
divNorm	0.028	0.003	0.032
divideChannels	0.006	0.002	0.008
eraseDataSetColumn	0.022	0.002	0.023
findReplicates	0.011	0.003	0.014
furthestFromZero	0.007	0.001	0.009
generateDatasetFile	0.021	0.001	0.023
generateRepMatNoFilter	0.013	0.001	0.015
generateReplicateMat	0.019	0.001	0.020
gseaAnalysis	4.377	0.081	16.523
hitselectionPval	0.064	0.003	0.067
hitselectionZscore	0.069	0.004	0.073
hitselectionZscorePval	0.070	0.004	0.074
incorporatepValVec	0.051	0.004	0.056
indexSubset	0.009	0.002	0.011
joinDatasetFiles	0.034	0.004	0.048
joinDatasets	0.010	0.001	0.012
lowessNorm	0.204	0.004	0.208
mainAnalysis	53.188	2.727	61.335
makeBoxplot4PlateType	0.106	0.011	0.119
makeBoxplotControls	0.067	0.007	0.075
makeBoxplotControlsPerPlate	0.204	0.013	0.217
makeBoxplotControlsPerScreen	0.112	0.008	0.121
makeBoxplotPerPlate	0.104	0.008	0.112
makeBoxplotPerScreen	0.065	0.007	0.073
multTestAdjust	0.008	0.002	0.010
numCellQualControl	0.056	0.006	0.063
orderGeneIDs	0.154	0.004	0.158
percCellQualControl	0.055	0.006	0.076
plotBar	0.245	0.008	0.254
plotControlHisto	0.158	0.007	0.166
plotControlHistoPerplate	0.635	0.015	0.652
plotControlHistoPerscreen	0.322	0.010	0.332
plotHisto	0.051	0.008	0.058
plotHistoPerplate	0.175	0.015	0.189
plotHistoPerscreen	0.275	0.010	0.285
plotQQ	0.052	0.007	0.059
plotQQperplate	0.177	0.013	0.191
plotQQperscreen	0.098	0.009	0.107
quantileNormalization	0.049	0.004	0.053
replicatesCV	0.109	0.009	0.118
replicatesSpearmancor	0.049	0.007	0.072
rms	0.008	0.002	0.010
rnaither	24.602	1.112	26.152
saveDataset	0.047	0.004	0.052
saveOldIntensityColumns	0.010	0.002	0.012
savepValVec	0.009	0.003	0.011
spatialDistrib	1.039	0.042	1.084
spatialDistribHits	1.117	0.047	1.166
subtractBackground	0.018	0.004	0.022
sumChannels	0.039	0.004	0.043
summarizeReps	0.133	0.003	0.136
summarizeRepsNoFiltering	0.141	0.002	0.144
trim	0.015	0.004	0.019
varAdjust	0.023	0.004	0.028
vennDiag	0.194	0.016	0.209
volcanoPlot	0.123	0.011	0.134