Package: RNAither

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings RNAither_1.8.1.tar.gz

StartedAt: 2010-10-04 18:31:56 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 18:36:33 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 277.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/RNAither.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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	0.221	0.005	0.232
DRQualControl	0.120	0.006	0.133
LiWongRank	0.240	0.007	0.248
MannWhitney	0.092	0.004	0.096
RankProduct	1.091	0.008	1.102
SNRQualControl	0.049	0.006	0.056
Ttest	0.092	0.003	0.096
ZPRIMEQualControl	0.071	0.010	0.114
ZScore	0.039	0.003	0.042
ZScorePerScreen	0.021	0.002	0.024
ZScorePlot	0.162	0.009	0.177
ZScorePlotTwo	0.048	0.006	0.062
channelPlot	0.060	0.006	0.069
closestToZero	0.006	0.001	0.008
compareHits	0.125	0.006	0.136
compareReplicaPlates	0.042	0.003	0.047
compareReplicateSD	0.381	0.015	0.409
compareReplicateSDPerScreen	0.707	0.027	0.749
compareReplicates	0.298	0.013	0.321
controlDensity	0.090	0.008	0.111
controlDensityPerPlate	0.329	0.019	0.353
controlDensityPerScreen	0.153	0.011	0.165
controlNorm	0.032	0.003	0.035
createSubset	0.007	0.001	0.009
discardLabtek	0.007	0.001	0.009
discardWells	0.010	0.002	0.011
divNorm	0.032	0.003	0.036
divideChannels	0.006	0.002	0.007
eraseDataSetColumn	0.179	0.002	0.181
findReplicates	0.009	0.002	0.012
furthestFromZero	0.006	0.001	0.007
generateDatasetFile	0.022	0.002	0.029
generateRepMatNoFilter	0.027	0.002	0.037
generateReplicateMat	0.034	0.001	0.038
gseaAnalysis	4.870	0.085	9.656
hitselectionPval	0.058	0.003	0.062
hitselectionZscore	0.068	0.004	0.071
hitselectionZscorePval	0.076	0.003	0.079
incorporatepValVec	0.061	0.004	0.064
indexSubset	0.007	0.001	0.008
joinDatasetFiles	0.034	0.004	0.040
joinDatasets	0.009	0.002	0.011
lowessNorm	0.029	0.004	0.033
mainAnalysis	57.350	2.796	71.299
makeBoxplot4PlateType	0.106	0.011	0.176
makeBoxplotControls	0.075	0.009	0.085
makeBoxplotControlsPerPlate	0.215	0.014	0.234
makeBoxplotControlsPerScreen	0.126	0.009	0.139
makeBoxplotPerPlate	0.110	0.008	0.119
makeBoxplotPerScreen	0.057	0.006	0.064
multTestAdjust	0.008	0.001	0.009
numCellQualControl	0.059	0.007	0.077
orderGeneIDs	0.222	0.005	0.233
percCellQualControl	0.057	0.007	0.075
plotBar	0.250	0.009	0.261
plotControlHisto	0.159	0.008	0.173
plotControlHistoPerplate	0.673	0.015	0.701
plotControlHistoPerscreen	0.340	0.009	0.351
plotHisto	0.049	0.007	0.077
plotHistoPerplate	0.175	0.013	0.190
plotHistoPerscreen	0.090	0.007	0.099
plotQQ	0.064	0.007	0.072
plotQQperplate	0.186	0.015	0.208
plotQQperscreen	0.095	0.010	0.109
quantileNormalization	0.055	0.005	0.060
replicatesCV	0.128	0.009	0.140
replicatesSpearmancor	0.054	0.006	0.067
rms	0.008	0.002	0.009
saveDataset	0.042	0.005	0.047
saveOldIntensityColumns	0.010	0.002	0.018
savepValVec	0.009	0.002	0.011
spatialDistrib	1.170	0.048	1.240
spatialDistribHits	1.399	0.050	1.482
subtractBackground	0.016	0.004	0.026
sumChannels	0.040	0.004	0.043
summarizeReps	0.173	0.002	0.176
summarizeRepsNoFiltering	0.159	0.003	0.162
trim	0.014	0.004	0.021
varAdjust	0.026	0.005	0.035
vennDiag	0.194	0.015	0.216
volcanoPlot	0.124	0.013	0.138