Package: RNAither

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.0.0.tar.gz

StartedAt: 2011-10-20 17:04:15 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:10:41 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 386.3 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/RNAither.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.0.0'
* checking package namespace 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (RNAither)

name	user	system	elapsed
BScore	0.074	0.006	0.082
DRQualControl	0.119	0.006	0.127
LiWongRank	0.292	0.004	0.296
MannWhitney	0.073	0.008	0.087
RankProduct	0.870	0.008	0.888
SNRQualControl	0.049	0.008	0.062
Ttest	0.076	0.005	0.090
ZPRIMEQualControl	0.065	0.011	0.086
ZScore	0.025	0.003	0.028
ZScorePerScreen	0.017	0.003	0.020
ZScorePlot	0.156	0.009	0.167
ZScorePlotTwo	0.047	0.006	0.053
channelPlot	0.052	0.006	0.058
closestToZero	0.006	0.001	0.007
compareHits	0.109	0.007	0.116
compareReplicaPlates	0.035	0.003	0.043
compareReplicateSD	0.332	0.014	0.355
compareReplicateSDPerScreen	0.498	0.022	0.522
compareReplicates	0.282	0.014	0.298
controlDensity	0.084	0.011	0.106
controlDensityPerPlate	0.312	0.020	0.332
controlDensityPerScreen	0.141	0.010	0.152
controlNorm	0.026	0.003	0.031
createSubset	0.011	0.002	0.012
discardLabtek	0.008	0.002	0.012
discardWells	0.008	0.002	0.009
divNorm	0.024	0.002	0.026
divideChannels	0.006	0.001	0.007
eraseDataSetColumn	0.020	0.001	0.021
findReplicates	0.010	0.002	0.012
furthestFromZero	0.005	0.001	0.006
generateDatasetFile	0.018	0.002	0.020
generateRepMatNoFilter	0.012	0.002	0.014
generateReplicateMat	0.028	0.002	0.029
gseaAnalysis	5.462	0.093	38.320
hitselectionPval	0.055	0.003	0.058
hitselectionZscore	0.057	0.003	0.062
hitselectionZscorePval	0.063	0.004	0.067
incorporatepValVec	0.040	0.004	0.044
indexSubset	0.006	0.001	0.007
joinDatasetFiles	0.031	0.004	0.035
joinDatasets	0.008	0.001	0.010
lowessNorm	0.032	0.003	0.035
mainAnalysis	57.117	2.890	66.697
makeBoxplot4PlateType	0.097	0.012	0.110
makeBoxplotControls	0.055	0.007	0.063
makeBoxplotControlsPerPlate	0.203	0.015	0.220
makeBoxplotControlsPerScreen	0.105	0.009	0.115
makeBoxplotPerPlate	0.101	0.009	0.191
makeBoxplotPerScreen	0.059	0.008	0.766
multTestAdjust	0.006	0.002	0.008
numCellQualControl	0.049	0.007	0.057
orderGeneIDs	0.137	0.004	0.142
percCellQualControl	0.052	0.008	0.060
plotBar	0.220	0.008	0.229
plotControlHisto	0.146	0.008	0.155
plotControlHistoPerplate	0.610	0.016	0.629
plotControlHistoPerscreen	0.313	0.010	0.323
plotHisto	0.046	0.008	0.054
plotHistoPerplate	0.167	0.014	0.181
plotHistoPerscreen	0.091	0.009	0.100
plotQQ	0.048	0.006	0.054
plotQQperplate	0.176	0.015	0.193
plotQQperscreen	0.088	0.009	0.097
quantileNormalization	0.043	0.005	0.048
replicatesCV	0.104	0.009	0.113
replicatesSpearmancor	0.042	0.006	0.048
rms	0.006	0.002	0.008
rnaither	21.864	0.973	24.908
saveDataset	0.034	0.005	0.038
saveOldIntensityColumns	0.008	0.002	0.010
savepValVec	0.007	0.003	0.009
spatialDistrib	1.042	0.049	1.180
spatialDistribHits	1.082	0.047	1.134
subtractBackground	0.012	0.004	0.017
sumChannels	0.029	0.004	0.033
summarizeReps	0.120	0.002	0.122
summarizeRepsNoFiltering	0.132	0.002	0.134
trim	0.011	0.004	0.016
varAdjust	0.018	0.005	0.023
vennDiag	0.165	0.016	0.660
volcanoPlot	0.123	0.011	0.134