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: 2011-03-31 08:17:21 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 08:22:47 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 326.0 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 1.1-00)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RNAither)

name	user	system	elapsed
BScore	0.044	0.008	0.052
DRQualControl	0.080	0.004	0.085
LiWongRank	0.14	0.00	0.14
MannWhitney	0.056	0.000	0.057
RankProduct	0.776	0.004	0.781
SNRQualControl	0.032	0.000	0.033
Ttest	0.060	0.000	0.059
ZPRIMEQualControl	0.064	0.000	0.122
ZScore	0.020	0.000	0.025
ZScorePerScreen	0.016	0.000	0.014
ZScorePlot	0.060	0.012	0.077
ZScorePlotTwo	0.032	0.004	0.039
channelPlot	0.036	0.004	0.040
closestToZero	0.004	0.000	0.005
compareHits	0.084	0.000	0.082
compareReplicaPlates	0.028	0.000	0.026
compareReplicateSD	0.212	0.004	0.216
compareReplicateSDPerScreen	0.280	0.000	0.278
compareReplicates	0.136	0.000	0.136
controlDensity	0.052	0.012	0.063
controlDensityPerPlate	0.180	0.008	0.186
controlDensityPerScreen	0.076	0.004	0.078
controlNorm	0.024	0.000	0.026
createSubset	0.004	0.000	0.005
discardLabtek	0.008	0.000	0.006
discardWells	0.008	0.000	0.007
divNorm	0.02	0.00	0.02
divideChannels	0.004	0.000	0.004
eraseDataSetColumn	0.016	0.000	0.014
findReplicates	0.008	0.000	0.007
furthestFromZero	0.004	0.000	0.004
generateDatasetFile	0.012	0.000	0.013
generateRepMatNoFilter	0.020	0.000	0.018
generateReplicateMat	0.024	0.004	0.028
gseaAnalysis	4.608	0.016	70.695
hitselectionPval	0.036	0.000	0.037
hitselectionZscore	0.040	0.000	0.042
hitselectionZscorePval	0.048	0.000	0.047
incorporatepValVec	0.036	0.004	0.038
indexSubset	0.004	0.000	0.005
joinDatasetFiles	0.020	0.004	0.023
joinDatasets	0.008	0.000	0.007
lowessNorm	0.016	0.004	0.019
mainAnalysis	32.466	0.388	93.131
makeBoxplot4PlateType	0.056	0.008	0.066
makeBoxplotControls	0.036	0.004	0.043
makeBoxplotControlsPerPlate	0.116	0.000	0.117
makeBoxplotControlsPerScreen	0.060	0.004	0.065
makeBoxplotPerPlate	0.056	0.004	0.062
makeBoxplotPerScreen	0.036	0.000	0.038
multTestAdjust	0.016	0.000	0.013
numCellQualControl	0.040	0.004	0.045
orderGeneIDs	0.124	0.004	0.128
percCellQualControl	0.040	0.004	0.042
plotBar	0.152	0.008	0.489
plotControlHisto	0.088	0.004	0.092
plotControlHistoPerplate	0.380	0.004	0.384
plotControlHistoPerscreen	0.196	0.000	0.196
plotHisto	0.024	0.000	0.026
plotHistoPerplate	0.076	0.008	0.083
plotHistoPerscreen	0.048	0.000	0.046
plotQQ	0.036	0.000	0.035
plotQQperplate	0.104	0.000	0.103
plotQQperscreen	0.049	0.008	0.056
quantileNormalization	0.032	0.000	0.036
replicatesCV	0.056	0.004	0.061
replicatesSpearmancor	0.028	0.008	0.037
rms	0.004	0.000	0.006
saveDataset	0.040	0.000	0.043
saveOldIntensityColumns	0.004	0.004	0.007
savepValVec	0.008	0.000	0.008
spatialDistrib	0.832	0.008	0.838
spatialDistribHits	0.608	0.000	0.610
subtractBackground	0.012	0.000	0.013
sumChannels	0.028	0.000	0.025
summarizeReps	0.108	0.000	0.109
summarizeRepsNoFiltering	0.100	0.000	0.096
trim	0.008	0.004	0.011
varAdjust	0.020	0.000	0.017
vennDiag	0.128	0.000	0.127
volcanoPlot	0.068	0.004	0.073