Package: RNAither

Version: 2.1.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.1.0.tar.gz

StartedAt: 2011-05-09 16:44:12 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:50:16 -0700 (Mon, 09 May 2011)

EllapsedTime: 364.1 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/RNAither.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... 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	0.077	0.006	0.083
DRQualControl	0.153	0.008	0.167
LiWongRank	0.176	0.007	0.189
MannWhitney	0.229	0.005	0.257
RankProduct	0.897	0.019	0.933
SNRQualControl	0.048	0.006	0.054
Ttest	0.067	0.004	0.072
ZPRIMEQualControl	0.067	0.012	0.089
ZScore	0.035	0.004	0.038
ZScorePerScreen	0.021	0.004	0.025
ZScorePlot	0.159	0.011	0.173
ZScorePlotTwo	0.049	0.006	0.056
channelPlot	0.055	0.006	0.063
closestToZero	0.006	0.002	0.008
compareHits	0.113	0.007	0.120
compareReplicaPlates	0.046	0.005	0.051
compareReplicateSD	0.332	0.017	0.354
compareReplicateSDPerScreen	0.513	0.026	0.542
compareReplicates	0.288	0.014	0.303
controlDensity	0.084	0.007	0.093
controlDensityPerPlate	0.315	0.018	0.335
controlDensityPerScreen	0.143	0.010	0.153
controlNorm	0.030	0.003	0.033
createSubset	0.007	0.002	0.010
discardLabtek	0.008	0.001	0.009
discardWells	0.009	0.001	0.011
divNorm	0.033	0.004	0.036
divideChannels	0.008	0.002	0.010
eraseDataSetColumn	0.021	0.001	0.023
findReplicates	0.011	0.003	0.014
furthestFromZero	0.007	0.001	0.007
generateDatasetFile	0.021	0.002	0.026
generateRepMatNoFilter	0.013	0.001	0.014
generateReplicateMat	0.019	0.001	0.020
gseaAnalysis	4.865	0.091	17.449
hitselectionPval	0.053	0.005	0.058
hitselectionZscore	0.060	0.006	0.066
hitselectionZscorePval	0.065	0.003	0.069
incorporatepValVec	0.042	0.004	0.046
indexSubset	0.006	0.001	0.008
joinDatasetFiles	0.033	0.003	0.037
joinDatasets	0.009	0.001	0.010
lowessNorm	0.033	0.003	0.036
mainAnalysis	54.420	2.862	63.332
makeBoxplot4PlateType	0.105	0.011	0.117
makeBoxplotControls	0.060	0.008	0.068
makeBoxplotControlsPerPlate	0.215	0.014	0.238
makeBoxplotControlsPerScreen	0.109	0.008	0.118
makeBoxplotPerPlate	0.106	0.009	0.116
makeBoxplotPerScreen	0.058	0.007	0.065
multTestAdjust	0.008	0.002	0.010
numCellQualControl	0.066	0.007	0.073
orderGeneIDs	0.150	0.004	0.154
percCellQualControl	0.052	0.006	0.063
plotBar	0.246	0.009	0.256
plotControlHisto	0.147	0.008	0.156
plotControlHistoPerplate	0.640	0.016	0.658
plotControlHistoPerscreen	0.502	0.010	0.512
plotHisto	0.049	0.008	0.057
plotHistoPerplate	0.171	0.013	0.185
plotHistoPerscreen	0.092	0.010	0.103
plotQQ	0.051	0.007	0.059
plotQQperplate	0.176	0.015	0.193
plotQQperscreen	0.093	0.009	0.102
quantileNormalization	0.046	0.005	0.052
replicatesCV	0.108	0.010	0.117
replicatesSpearmancor	0.048	0.006	0.063
rms	0.009	0.003	0.011
rnaither	22.003	0.966	23.607
saveDataset	0.037	0.004	0.042
saveOldIntensityColumns	0.010	0.002	0.012
savepValVec	0.010	0.003	0.014
spatialDistrib	1.062	0.048	1.172
spatialDistribHits	1.088	0.048	1.140
subtractBackground	0.017	0.004	0.021
sumChannels	0.038	0.004	0.042
summarizeReps	0.137	0.002	0.140
summarizeRepsNoFiltering	0.129	0.003	0.132
trim	0.015	0.004	0.019
varAdjust	0.023	0.005	0.027
vennDiag	0.188	0.016	0.205
volcanoPlot	0.121	0.011	0.131