Package: RNAither

Version: 1.10.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_1.10.0.tar.gz

StartedAt: 2011-04-07 08:43:30 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 08:48:17 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 287.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/RNAither.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-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 1.2-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RNAither)

name	user	system	elapsed
BScore	0.052	0.004	0.053
DRQualControl	0.080	0.004	0.082
LiWongRank	0.136	0.004	0.139
MannWhitney	0.056	0.000	0.058
RankProduct	0.768	0.008	0.778
SNRQualControl	0.024	0.008	0.033
Ttest	0.06	0.00	0.06
ZPRIMEQualControl	0.064	0.000	0.132
ZScore	0.020	0.004	0.020
ZScorePerScreen	0.012	0.000	0.014
ZScorePlot	0.072	0.000	0.072
ZScorePlotTwo	0.040	0.000	0.038
channelPlot	0.04	0.00	0.04
closestToZero	0.000	0.004	0.004
compareHits	0.072	0.008	0.083
compareReplicaPlates	0.024	0.004	0.026
compareReplicateSD	0.212	0.008	0.217
compareReplicateSDPerScreen	0.276	0.004	0.279
compareReplicates	0.128	0.004	0.134
controlDensity	0.056	0.004	0.063
controlDensityPerPlate	0.184	0.000	0.184
controlDensityPerScreen	0.076	0.004	0.078
controlNorm	0.028	0.000	0.027
createSubset	0.004	0.000	0.004
discardLabtek	0.004	0.004	0.005
discardWells	0.008	0.000	0.007
divNorm	0.02	0.00	0.02
divideChannels	0.004	0.000	0.005
eraseDataSetColumn	0.012	0.000	0.013
findReplicates	0.004	0.004	0.008
furthestFromZero	0.004	0.000	0.004
generateDatasetFile	0.012	0.000	0.013
generateRepMatNoFilter	0.020	0.000	0.019
generateReplicateMat	0.028	0.000	0.028
gseaAnalysis	4.576	0.020	46.266
hitselectionPval	0.032	0.008	0.037
hitselectionZscore	0.044	0.000	0.043
hitselectionZscorePval	0.048	0.000	0.048
incorporatepValVec	0.040	0.000	0.038
indexSubset	0.004	0.000	0.005
joinDatasetFiles	0.016	0.004	0.023
joinDatasets	0.004	0.000	0.006
lowessNorm	0.020	0.000	0.019
mainAnalysis	32.514	0.448	80.203
makeBoxplot4PlateType	0.052	0.008	0.057
makeBoxplotControls	0.036	0.000	0.037
makeBoxplotControlsPerPlate	0.108	0.004	0.113
makeBoxplotControlsPerScreen	0.068	0.000	0.065
makeBoxplotPerPlate	0.072	0.004	0.075
makeBoxplotPerScreen	0.028	0.008	0.034
multTestAdjust	0.000	0.004	0.006
numCellQualControl	0.036	0.000	0.038
orderGeneIDs	0.124	0.004	0.124
percCellQualControl	0.032	0.004	0.037
plotBar	0.148	0.004	0.153
plotControlHisto	0.080	0.004	0.084
plotControlHistoPerplate	0.364	0.000	0.366
plotControlHistoPerscreen	0.192	0.000	0.193
plotHisto	0.032	0.000	0.033
plotHistoPerplate	0.084	0.004	0.088
plotHistoPerscreen	0.040	0.004	0.046
plotQQ	0.032	0.000	0.035
plotQQperplate	0.088	0.000	0.090
plotQQperscreen	0.053	0.000	0.054
quantileNormalization	0.040	0.000	0.041
replicatesCV	0.06	0.00	0.06
replicatesSpearmancor	0.028	0.004	0.035
rms	0.004	0.000	0.006
saveDataset	0.024	0.004	0.027
saveOldIntensityColumns	0.008	0.000	0.007
savepValVec	0.008	0.000	0.007
spatialDistrib	0.576	0.000	0.575
spatialDistribHits	0.632	0.008	0.640
subtractBackground	0.008	0.004	0.013
sumChannels	0.024	0.004	0.024
summarizeReps	0.108	0.000	0.109
summarizeRepsNoFiltering	0.096	0.000	0.097
trim	0.008	0.004	0.012
varAdjust	0.016	0.000	0.019
vennDiag	0.120	0.004	0.124
volcanoPlot	0.072	0.000	0.073