Package: RNAither

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_1.10.0.tar.gz

StartedAt: 2011-03-31 07:38:07 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 07:45:16 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 429.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/RNAither.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* 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 ‘1.10.0’
* 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
  '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	0.078	0.006	0.084
DRQualControl	0.134	0.006	0.148
LiWongRank	0.215	0.004	0.223
MannWhitney	0.092	0.005	0.104
RankProduct	1.034	0.013	1.056
SNRQualControl	0.047	0.006	0.054
Ttest	0.081	0.003	0.084
ZPRIMEQualControl	0.068	0.011	0.090
ZScore	0.037	0.003	0.043
ZScorePerScreen	0.021	0.003	0.024
ZScorePlot	0.165	0.010	0.184
ZScorePlotTwo	0.049	0.006	0.060
channelPlot	0.055	0.006	0.069
closestToZero	0.007	0.001	0.008
compareHits	0.121	0.009	0.139
compareReplicaPlates	0.047	0.004	0.055
compareReplicateSD	0.349	0.016	0.380
compareReplicateSDPerScreen	0.506	0.021	0.542
compareReplicates	0.289	0.013	0.315
controlDensity	0.089	0.008	0.100
controlDensityPerPlate	0.325	0.020	0.358
controlDensityPerScreen	0.147	0.011	0.163
controlNorm	0.032	0.003	0.036
createSubset	0.008	0.002	0.010
discardLabtek	0.008	0.002	0.010
discardWells	0.010	0.001	0.012
divNorm	0.036	0.003	0.039
divideChannels	0.006	0.002	0.008
eraseDataSetColumn	0.022	0.001	0.024
findReplicates	0.011	0.002	0.013
furthestFromZero	0.007	0.001	0.008
generateDatasetFile	0.021	0.002	0.023
generateRepMatNoFilter	0.027	0.002	0.029
generateReplicateMat	0.034	0.001	0.035
gseaAnalysis	4.791	0.104	67.696
hitselectionPval	0.057	0.005	0.065
hitselectionZscore	0.072	0.004	0.084
hitselectionZscorePval	0.063	0.004	0.072
incorporatepValVec	0.060	0.005	0.068
indexSubset	0.007	0.001	0.009
joinDatasetFiles	0.035	0.004	0.048
joinDatasets	0.010	0.001	0.016
lowessNorm	0.039	0.003	0.049
mainAnalysis	55.903	2.853	116.185
makeBoxplot4PlateType	0.102	0.011	0.114
makeBoxplotControls	0.061	0.007	0.070
makeBoxplotControlsPerPlate	0.218	0.015	0.278
makeBoxplotControlsPerScreen	0.112	0.009	0.124
makeBoxplotPerPlate	0.105	0.009	0.120
makeBoxplotPerScreen	0.056	0.006	0.065
multTestAdjust	0.008	0.002	0.009
numCellQualControl	0.060	0.008	0.078
orderGeneIDs	0.188	0.005	0.196
percCellQualControl	0.055	0.007	0.074
plotBar	0.241	0.009	0.263
plotControlHisto	0.148	0.008	0.180
plotControlHistoPerplate	0.622	0.016	0.655
plotControlHistoPerscreen	0.319	0.010	0.343
plotHisto	0.048	0.007	0.060
plotHistoPerplate	0.176	0.014	0.200
plotHistoPerscreen	0.098	0.010	0.117
plotQQ	0.052	0.007	0.066
plotQQperplate	0.177	0.014	0.208
plotQQperscreen	0.099	0.010	0.121
quantileNormalization	0.051	0.005	0.069
replicatesCV	0.114	0.009	0.130
replicatesSpearmancor	0.052	0.006	0.062
rms	0.008	0.002	0.010
saveDataset	0.047	0.005	0.055
saveOldIntensityColumns	0.010	0.002	0.012
savepValVec	0.010	0.003	0.016
spatialDistrib	1.051	0.053	1.271
spatialDistribHits	1.104	0.048	1.216
subtractBackground	0.024	0.005	0.038
sumChannels	0.038	0.004	0.043
summarizeReps	0.159	0.003	0.162
summarizeRepsNoFiltering	0.158	0.003	0.161
trim	0.015	0.004	0.020
varAdjust	0.027	0.004	0.034
vennDiag	0.186	0.019	0.220
volcanoPlot	0.140	0.014	0.181