BioC 2.12: CHECK report for RNAither on george2

Package: RNAither

Version: 2.8.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.8.0.tar.gz

StartedAt: 2013-10-09 04:40:30 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:48:36 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 485.9 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.8.0’
* 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 ... [38s/42s] 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [105s/113s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 48.947  1.560  54.147
rnaither     14.785  0.172  15.310
gseaAnalysis 10.308  0.036  13.351
* 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
  ‘/home/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
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.092	0.008	0.142
DRQualControl	0.072	0.000	0.071
LiWongRank	0.148	0.000	0.147
MannWhitney	0.097	0.004	0.101
RankProduct	1.248	0.020	1.291
SNRQualControl	0.076	0.008	0.087
Ttest	0.100	0.000	0.099
ZPRIMEQualControl	0.124	0.004	0.127
ZScore	0.060	0.004	0.065
ZScorePerScreen	0.656	0.004	0.660
ZScorePlot	0.088	0.008	0.096
ZScorePlotTwo	0.064	0.004	0.068
channelPlot	0.064	0.004	0.071
closestToZero	0.032	0.004	0.036
compareHits	0.140	0.008	0.147
compareReplicaPlates	0.056	0.008	0.064
compareReplicateSD	0.320	0.012	0.330
compareReplicateSDPerScreen	0.460	0.004	0.463
compareReplicates	0.180	0.008	0.607
controlDensity	0.128	0.008	0.139
controlDensityPerPlate	0.244	0.004	0.251
controlDensityPerScreen	0.132	0.004	0.134
controlNorm	0.056	0.004	0.061
createSubset	0.032	0.000	0.030
discardLabtek	0.032	0.000	0.031
discardWells	0.028	0.004	0.031
divNorm	0.088	0.004	0.092
divideChannels	0.032	0.004	0.033
eraseDataSetColumn	0.032	0.000	0.032
findReplicates	0.028	0.000	0.027
furthestFromZero	0.032	0.000	0.033
generateDatasetFile	0.096	0.004	0.099
generateRepMatNoFilter	0.028	0.000	0.029
generateReplicateMat	0.036	0.000	0.035
gseaAnalysis	10.308	0.036	13.351
hitselectionPval	0.104	0.016	0.164
hitselectionZscore	0.084	0.004	0.096
hitselectionZscorePval	0.073	0.004	0.081
incorporatepValVec	0.088	0.000	0.087
indexSubset	0.024	0.004	0.029
joinDatasetFiles	0.084	0.000	0.085
joinDatasets	0.036	0.000	0.033
lowessNorm	0.056	0.004	0.067
mainAnalysis	48.947	1.560	54.147
makeBoxplot4PlateType	0.100	0.020	0.119
makeBoxplotControls	0.080	0.004	0.084
makeBoxplotControlsPerPlate	0.196	0.008	0.205
makeBoxplotControlsPerScreen	0.112	0.000	0.113
makeBoxplotPerPlate	0.104	0.000	0.103
makeBoxplotPerScreen	0.084	0.004	0.086
multTestAdjust	0.028	0.000	0.028
numCellQualControl	0.08	0.00	0.08
orderGeneIDs	0.876	0.000	0.876
percCellQualControl	0.056	0.000	0.058
plotBar	0.164	0.000	0.165
plotControlHisto	0.104	0.000	0.102
plotControlHistoPerplate	0.392	0.004	0.399
plotControlHistoPerscreen	0.220	0.000	0.219
plotHisto	0.044	0.004	0.050
plotHistoPerplate	0.136	0.004	0.140
plotHistoPerscreen	0.068	0.008	0.076
plotQQ	0.056	0.000	0.056
plotQQperplate	0.108	0.012	0.120
plotQQperscreen	0.080	0.000	0.079
quantileNormalization	0.056	0.004	0.060
replicatesCV	0.084	0.012	0.094
replicatesSpearmancor	0.056	0.008	0.062
rms	0.020	0.004	0.023
rnaither	14.785	0.172	15.310
saveDataset	0.056	0.012	0.069
saveOldIntensityColumns	0.028	0.004	0.032
savepValVec	0.032	0.004	0.034
spatialDistrib	0.724	0.024	0.746
spatialDistribHits	0.812	0.016	0.828
subtractBackground	0.032	0.008	0.039
sumChannels	0.052	0.004	0.054
summarizeReps	0.132	0.004	0.136
summarizeRepsNoFiltering	0.144	0.000	0.144
trim	0.040	0.004	0.048
varAdjust	0.052	0.004	0.054
vennDiag	0.200	0.012	0.211
volcanoPlot	0.132	0.008	0.140