BioC 2.11: CHECK report for RNAither on lamb1

Package: RNAither

Version: 2.6.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.6.0.tar.gz

StartedAt: 2013-03-25 04:31:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:37:37 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 387.5 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/RNAither.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.6.0’
* 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 for left-over 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
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 33.846  0.832  42.400
rnaither     10.137  0.116  11.430
gseaAnalysis  5.149  0.048   8.119
* 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/biocbuild/bbs-2.11-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	0.040	0.012	0.055
DRQualControl	0.040	0.008	0.047
LiWongRank	0.092	0.000	0.093
MannWhitney	0.044	0.000	0.046
RankProduct	0.812	0.020	0.850
SNRQualControl	0.036	0.008	0.082
Ttest	0.040	0.008	0.051
ZPRIMEQualControl	0.080	0.008	1.017
ZScore	0.032	0.000	0.067
ZScorePerScreen	0.016	0.000	0.026
ZScorePlot	0.076	0.000	0.156
ZScorePlotTwo	0.028	0.004	0.059
channelPlot	0.032	0.008	0.100
closestToZero	0.004	0.000	0.016
compareHits	0.076	0.004	0.118
compareReplicaPlates	0.032	0.000	0.077
compareReplicateSD	0.208	0.004	0.226
compareReplicateSDPerScreen	0.300	0.008	0.307
compareReplicates	0.148	0.000	0.148
controlDensity	0.072	0.000	0.104
controlDensityPerPlate	0.176	0.000	0.328
controlDensityPerScreen	0.088	0.008	0.185
controlNorm	0.020	0.000	0.018
createSubset	0.008	0.000	0.006
discardLabtek	0.008	0.000	0.007
discardWells	0.008	0.000	0.007
divNorm	0.012	0.004	0.019
divideChannels	0.004	0.000	0.006
eraseDataSetColumn	0.016	0.000	0.015
findReplicates	0.008	0.000	0.009
furthestFromZero	0.008	0.000	0.005
generateDatasetFile	0.012	0.000	0.013
generateRepMatNoFilter	0.012	0.000	0.032
generateReplicateMat	0.016	0.004	0.036
gseaAnalysis	5.149	0.048	8.119
hitselectionPval	0.036	0.000	0.035
hitselectionZscore	0.048	0.004	0.055
hitselectionZscorePval	0.036	0.000	0.037
incorporatepValVec	0.020	0.004	0.027
indexSubset	0.004	0.000	0.006
joinDatasetFiles	0.024	0.004	0.097
joinDatasets	0.008	0.000	0.015
lowessNorm	0.032	0.000	0.084
mainAnalysis	33.846	0.832	42.400
makeBoxplot4PlateType	0.076	0.000	0.127
makeBoxplotControls	0.048	0.000	0.048
makeBoxplotControlsPerPlate	0.108	0.004	0.140
makeBoxplotControlsPerScreen	0.060	0.000	0.079
makeBoxplotPerPlate	0.056	0.000	0.058
makeBoxplotPerScreen	0.024	0.008	0.123
multTestAdjust	0.004	0.000	0.007
numCellQualControl	0.040	0.004	0.082
orderGeneIDs	0.060	0.008	0.090
percCellQualControl	0.036	0.004	0.062
plotBar	0.124	0.004	0.177
plotControlHisto	0.064	0.000	0.113
plotControlHistoPerplate	0.268	0.008	0.303
plotControlHistoPerscreen	0.132	0.004	0.222
plotHisto	0.020	0.008	0.037
plotHistoPerplate	0.084	0.000	0.130
plotHistoPerscreen	0.052	0.004	0.115
plotQQ	0.032	0.000	0.059
plotQQperplate	0.080	0.004	0.087
plotQQperscreen	0.044	0.008	0.053
quantileNormalization	0.048	0.000	0.059
replicatesCV	0.060	0.000	0.091
replicatesSpearmancor	0.028	0.004	0.048
rms	0.004	0.004	0.006
rnaither	10.137	0.116	11.430
saveDataset	0.016	0.008	0.221
saveOldIntensityColumns	0.004	0.004	0.008
savepValVec	0.004	0.004	0.007
spatialDistrib	0.532	0.020	0.797
spatialDistribHits	0.532	0.020	0.550
subtractBackground	0.012	0.004	0.017
sumChannels	0.020	0.008	0.032
summarizeReps	0.072	0.004	0.076
summarizeRepsNoFiltering	0.072	0.008	0.081
trim	0.012	0.000	0.015
varAdjust	0.016	0.000	0.019
vennDiag	0.120	0.008	0.128
volcanoPlot	0.080	0.008	0.851

Summary

Command output