BioC 2.10: CHECK report for RNAither on petty

Package: RNAither

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.4.0.tar.gz

StartedAt: 2012-09-24 01:36:06 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:42:21 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 375.6 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/RNAither.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '2.4.0'
* 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 sizes of PDF files under 'inst/doc' ... 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
  '/Users/biocbuild/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.
** help
*** installing help indices
** building package indices
** installing vignettes
   'vignetteRNAither.Rnw' 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (RNAither)

name	user	system	elapsed
BScore	0.050	0.006	0.056
DRQualControl	0.029	0.007	0.037
LiWongRank	0.089	0.006	0.096
MannWhitney	0.044	0.005	0.049
RankProduct	0.643	0.009	0.652
SNRQualControl	0.031	0.010	0.041
Ttest	0.047	0.004	0.051
ZPRIMEQualControl	0.047	0.012	0.068
ZScore	0.017	0.004	0.020
ZScorePerScreen	0.011	0.004	0.015
ZScorePlot	0.119	0.009	0.131
ZScorePlotTwo	0.037	0.007	0.044
channelPlot	0.041	0.007	0.050
closestToZero	0.004	0.002	0.005
compareHits	0.080	0.010	0.089
compareReplicaPlates	0.023	0.006	0.029
compareReplicateSD	0.259	0.014	0.276
compareReplicateSDPerScreen	0.395	0.023	0.420
compareReplicates	0.410	0.014	0.426
controlDensity	0.091	0.011	0.103
controlDensityPerPlate	0.248	0.020	0.269
controlDensityPerScreen	0.112	0.013	0.125
controlNorm	0.020	0.004	0.025
createSubset	0.004	0.002	0.007
discardLabtek	0.005	0.002	0.006
discardWells	0.006	0.003	0.008
divNorm	0.022	0.004	0.027
divideChannels	0.004	0.003	0.007
eraseDataSetColumn	0.014	0.002	0.016
findReplicates	0.009	0.004	0.013
furthestFromZero	0.005	0.002	0.008
generateDatasetFile	0.012	0.001	0.017
generateRepMatNoFilter	0.009	0.003	0.011
generateReplicateMat	0.013	0.002	0.016
gseaAnalysis	5.507	0.131	8.098
hitselectionPval	0.056	0.006	0.063
hitselectionZscore	0.075	0.007	0.082
hitselectionZscorePval	0.039	0.004	0.043
incorporatepValVec	0.051	0.007	0.059
indexSubset	0.006	0.003	0.009
joinDatasetFiles	0.032	0.006	0.039
joinDatasets	0.007	0.002	0.010
lowessNorm	0.024	0.005	0.030
mainAnalysis	52.036	3.254	63.510
makeBoxplot4PlateType	0.084	0.014	0.099
makeBoxplotControls	0.044	0.009	0.053
makeBoxplotControlsPerPlate	0.173	0.017	0.190
makeBoxplotControlsPerScreen	0.079	0.011	0.090
makeBoxplotPerPlate	0.092	0.009	0.102
makeBoxplotPerScreen	0.043	0.008	0.051
multTestAdjust	0.004	0.003	0.007
numCellQualControl	0.036	0.008	0.051
orderGeneIDs	0.089	0.005	0.095
percCellQualControl	0.040	0.008	0.051
plotBar	0.176	0.010	0.187
plotControlHisto	0.084	0.010	0.094
plotControlHistoPerplate	0.357	0.016	0.373
plotControlHistoPerscreen	0.186	0.009	0.195
plotHisto	0.044	0.008	0.051
plotHistoPerplate	0.166	0.019	0.248
plotHistoPerscreen	0.066	0.009	0.075
plotQQ	0.037	0.008	0.044
plotQQperplate	0.126	0.014	0.139
plotQQperscreen	0.065	0.009	0.074
quantileNormalization	0.027	0.005	0.032
replicatesCV	0.076	0.011	0.087
replicatesSpearmancor	0.027	0.007	0.041
rms	0.004	0.002	0.006
rnaither	14.565	0.752	15.891
saveDataset	0.020	0.005	0.025
saveOldIntensityColumns	0.004	0.002	0.007
savepValVec	0.005	0.003	0.008
spatialDistrib	0.689	0.035	0.726
spatialDistribHits	0.741	0.037	0.780
subtractBackground	0.007	0.004	0.012
sumChannels	0.018	0.004	0.022
summarizeReps	0.080	0.002	0.082
summarizeRepsNoFiltering	0.095	0.003	0.098
trim	0.007	0.005	0.012
varAdjust	0.011	0.003	0.014
vennDiag	0.114	0.013	0.128
volcanoPlot	0.080	0.014	0.153

Summary

Command output