BioC 3.0: CHECK report for RNAither on zin1

Package: RNAither

Version: 2.14.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.14.0.tar.gz

StartedAt: 2015-04-10 03:53:47 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:59:28 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 341.0 seconds

RetCode: 0

Status:  OK

CheckDir: RNAither.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/RNAither.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.14.0’
* 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 ... [27s/27s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘RankProd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotSpatialDistrib: no visible global function definition for
  ‘brewer.pal’
RankProduct: no visible global function definition for ‘RP’
compareReplicateSD: no visible global function definition for
  ‘brewer.pal’
compareReplicateSDPerScreen: no visible global function definition for
  ‘brewer.pal’
spatialDistrib: no visible global function definition for ‘brewer.pal’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [60s/66s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 28.373  0.484  32.073
rnaither      9.128  0.072   9.309
gseaAnalysis  4.021  0.028   6.982
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	0.044	0.004	0.048
DRQualControl	0.024	0.012	0.035
LiWongRank	0.068	0.000	0.066
MannWhitney	0.040	0.000	0.041
RankProduct	0.384	0.004	0.388
SNRQualControl	0.032	0.004	0.034
Ttest	0.032	0.000	0.032
ZPRIMEQualControl	0.036	0.004	0.043
ZScore	0.012	0.000	0.016
ZScorePerScreen	0.012	0.000	0.012
ZScorePlot	0.048	0.004	0.050
ZScorePlotTwo	0.024	0.000	0.026
channelPlot	0.028	0.000	0.030
closestToZero	0.000	0.004	0.004
compareHits	0.064	0.004	0.067
compareReplicaPlates	0.020	0.004	0.026
compareReplicateSD	0.160	0.000	0.161
compareReplicateSDPerScreen	0.244	0.004	0.247
compareReplicates	0.120	0.000	0.119
controlDensity	0.052	0.000	0.053
controlDensityPerPlate	0.164	0.004	0.166
controlDensityPerScreen	0.072	0.000	0.071
controlNorm	0.012	0.000	0.016
createSubset	0.004	0.000	0.006
discardLabtek	0.004	0.000	0.006
discardWells	0.008	0.000	0.007
divNorm	0.020	0.000	0.017
divideChannels	0.004	0.000	0.004
eraseDataSetColumn	0.012	0.000	0.012
findReplicates	0.004	0.004	0.009
furthestFromZero	0.008	0.000	0.005
generateDatasetFile	0.012	0.004	0.015
generateRepMatNoFilter	0.012	0.000	0.009
generateReplicateMat	0.016	0.000	0.014
gseaAnalysis	4.021	0.028	6.982
hitselectionPval	0.028	0.004	0.034
hitselectionZscore	0.028	0.004	0.035
hitselectionZscorePval	0.028	0.004	0.034
incorporatepValVec	0.024	0.000	0.024
indexSubset	0.004	0.000	0.004
joinDatasetFiles	0.024	0.000	0.036
joinDatasets	0.000	0.004	0.005
lowessNorm	0.008	0.004	0.014
mainAnalysis	28.373	0.484	32.073
makeBoxplot4PlateType	0.040	0.008	0.048
makeBoxplotControls	0.032	0.000	0.032
makeBoxplotControlsPerPlate	0.092	0.000	0.091
makeBoxplotControlsPerScreen	0.048	0.000	0.049
makeBoxplotPerPlate	0.044	0.000	0.046
makeBoxplotPerScreen	0.028	0.000	0.028
multTestAdjust	0.008	0.000	0.006
numCellQualControl	0.032	0.004	0.044
orderGeneIDs	0.056	0.004	0.060
percCellQualControl	0.032	0.000	0.033
plotBar	0.104	0.004	0.106
plotControlHisto	0.056	0.008	0.062
plotControlHistoPerplate	0.252	0.004	0.255
plotControlHistoPerscreen	0.124	0.004	0.126
plotHisto	0.024	0.000	0.022
plotHistoPerplate	0.057	0.008	0.064
plotHistoPerscreen	0.044	0.000	0.042
plotQQ	0.028	0.000	0.026
plotQQperplate	0.068	0.000	0.069
plotQQperscreen	0.040	0.000	0.042
quantileNormalization	0.024	0.000	0.023
replicatesCV	0.044	0.000	0.044
replicatesSpearmancor	0.024	0.004	0.026
rms	0.004	0.000	0.006
rnaither	9.128	0.072	9.309
saveDataset	0.020	0.004	0.023
saveOldIntensityColumns	0.008	0.000	0.007
savepValVec	0.008	0.000	0.008
spatialDistrib	0.460	0.008	0.469
spatialDistribHits	0.464	0.008	0.474
subtractBackground	0.012	0.000	0.012
sumChannels	0.02	0.00	0.02
summarizeReps	0.080	0.004	0.085
summarizeRepsNoFiltering	0.076	0.000	0.079
trim	0.008	0.004	0.012
varAdjust	0.016	0.000	0.016
vennDiag	0.084	0.008	0.092
volcanoPlot	0.056	0.000	0.058