BioC 2.12: CHECK report for RNAither on petty

Package: RNAither

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.7.0.tar.gz

StartedAt: 2013-03-25 04:31:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:38:32 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 412.8 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.7.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'RNAither' can be installed ... [30s/31s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file 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 ... [108s/130s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 54.951  3.803  75.694
rnaither     18.744  1.087  20.279
gseaAnalysis  6.144  0.143   8.298
* 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-2.12-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	0.063	0.014	0.078
DRQualControl	0.042	0.017	0.075
LiWongRank	0.155	0.020	0.176
MannWhitney	0.087	0.018	0.106
RankProduct	0.577	0.027	0.605
SNRQualControl	0.063	0.027	0.092
Ttest	0.073	0.015	0.091
ZPRIMEQualControl	0.087	0.026	0.122
ZScore	0.044	0.015	0.070
ZScorePerScreen	0.032	0.019	0.064
ZScorePlot	0.201	0.026	0.233
ZScorePlotTwo	0.060	0.020	0.082
channelPlot	0.283	0.020	0.306
closestToZero	0.015	0.009	0.025
compareHits	0.090	0.022	0.112
compareReplicaPlates	0.031	0.013	0.046
compareReplicateSD	0.307	0.024	0.556
compareReplicateSDPerScreen	0.360	0.032	0.673
compareReplicates	0.216	0.021	0.423
controlDensity	0.080	0.018	0.153
controlDensityPerPlate	0.240	0.027	0.335
controlDensityPerScreen	0.124	0.022	0.448
controlNorm	0.031	0.014	0.046
createSubset	0.015	0.009	0.025
discardLabtek	0.014	0.012	0.036
discardWells	0.012	0.008	0.022
divNorm	0.031	0.015	0.047
divideChannels	0.010	0.008	0.018
eraseDataSetColumn	0.021	0.009	0.031
findReplicates	0.019	0.011	0.031
furthestFromZero	0.014	0.009	0.024
generateDatasetFile	0.041	0.024	0.076
generateRepMatNoFilter	0.018	0.008	0.026
generateReplicateMat	0.021	0.008	0.029
gseaAnalysis	6.144	0.143	8.298
hitselectionPval	0.074	0.014	0.091
hitselectionZscore	0.078	0.017	0.100
hitselectionZscorePval	0.067	0.015	0.085
incorporatepValVec	0.065	0.020	0.085
indexSubset	0.024	0.011	0.036
joinDatasetFiles	0.049	0.016	0.066
joinDatasets	0.021	0.010	0.031
lowessNorm	0.025	0.014	0.038
mainAnalysis	54.951	3.803	75.694
makeBoxplot4PlateType	0.090	0.022	0.113
makeBoxplotControls	0.063	0.017	0.081
makeBoxplotControlsPerPlate	0.172	0.025	0.197
makeBoxplotControlsPerScreen	0.104	0.018	0.124
makeBoxplotPerPlate	0.118	0.022	0.141
makeBoxplotPerScreen	0.058	0.016	0.076
multTestAdjust	0.017	0.009	0.026
numCellQualControl	0.055	0.017	0.087
orderGeneIDs	0.083	0.011	0.094
percCellQualControl	0.273	0.017	0.366
plotBar	0.180	0.021	0.291
plotControlHisto	0.112	0.018	0.134
plotControlHistoPerplate	0.406	0.025	0.431
plotControlHistoPerscreen	0.206	0.019	0.224
plotHisto	0.052	0.017	0.069
plotHistoPerplate	0.153	0.024	0.178
plotHistoPerscreen	0.082	0.018	0.100
plotQQ	0.046	0.017	0.065
plotQQperplate	0.150	0.023	0.173
plotQQperscreen	0.080	0.017	0.098
quantileNormalization	0.039	0.013	0.053
replicatesCV	0.090	0.017	0.109
replicatesSpearmancor	0.039	0.014	0.067
rms	0.016	0.012	0.033
rnaither	18.744	1.087	20.279
saveDataset	0.038	0.015	0.054
saveOldIntensityColumns	0.016	0.009	0.025
savepValVec	0.028	0.014	0.049
spatialDistrib	0.883	0.061	0.945
spatialDistribHits	0.922	0.066	0.994
subtractBackground	0.027	0.015	0.042
sumChannels	0.036	0.012	0.049
summarizeReps	0.309	0.010	0.320
summarizeRepsNoFiltering	0.099	0.010	0.109
trim	0.018	0.013	0.031
varAdjust	0.027	0.014	0.042
vennDiag	0.186	0.046	0.272
volcanoPlot	0.161	0.033	0.197

Summary

Command output