Package: RNAither

Version: 2.4.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.4.0.tar.gz

StartedAt: 2012-04-01 03:11:10 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:16:20 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 309.8 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/RNAither.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 installed files from '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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/RNAither.Rcheck/00check.log'
for details.

* 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
** installing vignettes
   'vignetteRNAither.Rnw' 
** 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	0.048	0.000	0.059
DRQualControl	0.032	0.000	0.044
LiWongRank	0.076	0.008	0.102
MannWhitney	0.036	0.004	0.053
RankProduct	0.408	0.000	0.420
SNRQualControl	0.040	0.000	0.051
Ttest	0.036	0.004	0.053
ZPRIMEQualControl	0.048	0.008	0.070
ZScore	0.020	0.004	0.036
ZScorePerScreen	0.016	0.004	0.030
ZScorePlot	0.052	0.016	0.088
ZScorePlotTwo	0.044	0.000	0.056
channelPlot	0.036	0.000	0.048
closestToZero	0.004	0.000	0.009
compareHits	0.076	0.008	0.107
compareReplicaPlates	0.028	0.000	0.039
compareReplicateSD	0.168	0.004	0.184
compareReplicateSDPerScreen	0.244	0.000	0.259
compareReplicates	0.112	0.008	0.131
controlDensity	0.060	0.000	0.078
controlDensityPerPlate	0.324	0.004	0.343
controlDensityPerScreen	0.072	0.004	0.091
controlNorm	0.016	0.000	0.029
createSubset	0.004	0.000	0.015
discardLabtek	0.008	0.000	0.013
discardWells	0.004	0.000	0.013
divNorm	0.020	0.004	0.035
divideChannels	0.008	0.000	0.013
eraseDataSetColumn	0.016	0.008	0.030
findReplicates	0.008	0.004	0.023
furthestFromZero	0.004	0.004	0.011
generateDatasetFile	0.016	0.000	0.015
generateRepMatNoFilter	0.012	0.000	0.019
generateReplicateMat	0.020	0.000	0.025
gseaAnalysis	3.532	0.024	41.545
hitselectionPval	0.044	0.000	0.058
hitselectionZscore	0.052	0.000	0.069
hitselectionZscorePval	0.048	0.000	0.060
incorporatepValVec	0.028	0.008	0.056
indexSubset	0.000	0.004	0.011
joinDatasetFiles	0.02	0.00	0.03
joinDatasets	0.008	0.000	0.014
lowessNorm	0.012	0.004	0.026
mainAnalysis	27.822	0.340	61.806
makeBoxplot4PlateType	0.056	0.000	0.065
makeBoxplotControls	0.036	0.000	0.047
makeBoxplotControlsPerPlate	0.104	0.000	0.115
makeBoxplotControlsPerScreen	0.06	0.00	0.07
makeBoxplotPerPlate	0.052	0.004	0.069
makeBoxplotPerScreen	0.040	0.000	0.049
multTestAdjust	0.004	0.000	0.010
numCellQualControl	0.032	0.008	0.055
orderGeneIDs	0.080	0.000	0.088
percCellQualControl	0.036	0.000	0.049
plotBar	0.128	0.004	0.144
plotControlHisto	0.068	0.004	0.086
plotControlHistoPerplate	0.284	0.000	0.296
plotControlHistoPerscreen	0.148	0.004	0.161
plotHisto	0.024	0.004	0.041
plotHistoPerplate	0.072	0.000	0.083
plotHistoPerscreen	0.040	0.000	0.053
plotQQ	0.024	0.000	0.038
plotQQperplate	0.072	0.004	0.084
plotQQperscreen	0.032	0.008	0.052
quantileNormalization	0.024	0.000	0.037
replicatesCV	0.044	0.004	0.061
replicatesSpearmancor	0.024	0.000	0.036
rms	0.004	0.004	0.010
rnaither	8.725	0.048	8.885
saveDataset	0.016	0.004	0.034
saveOldIntensityColumns	0.008	0.000	0.010
savepValVec	0.004	0.000	0.010
spatialDistrib	0.508	0.008	0.535
spatialDistribHits	0.500	0.012	0.533
subtractBackground	0.012	0.000	0.023
sumChannels	0.020	0.000	0.033
summarizeReps	0.088	0.000	0.091
summarizeRepsNoFiltering	0.076	0.004	0.085
trim	0.000	0.008	0.020
varAdjust	0.012	0.004	0.024
vennDiag	0.084	0.016	0.126
volcanoPlot	0.060	0.004	0.077