Multiple platform build/check report for BioC 3.8 - CHECK report for RNAither on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RNAither.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RNAither_2.30.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RNAither.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.30.1’
* 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 ... 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 dependencies in R code ... NOTE
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’
Undefined global functions or variables:
  RP 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 24.041  2.671  28.023
rnaither     15.323  1.625  18.564
gseaAnalysis  5.272  0.134  14.712
* 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

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/RNAither.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RNAither
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RNAither’ ...
** R
** data
** inst
** byte-compile and prepare 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)

Tests output

Example timings

name	user	system	elapsed
BScore	0.038	0.000	0.039
DRQualControl	0.022	0.002	0.025
LiWongRank	0.062	0.001	0.063
MannWhitney	0.032	0.000	0.033
RankProduct	0.112	0.005	0.117
SNRQualControl	0.024	0.004	0.028
Ttest	0.041	0.002	0.043
ZPRIMEQualControl	0.038	0.013	0.052
ZScore	0.015	0.001	0.016
ZScorePerScreen	0.010	0.001	0.011
ZScorePlot	0.117	0.030	0.160
ZScorePlotTwo	0.030	0.023	0.038
channelPlot	0.034	0.005	0.041
closestToZero	0.002	0.000	0.002
compareHits	0.036	0.001	0.037
compareReplicaPlates	0.014	0.002	0.015
compareReplicateSD	0.194	0.015	0.215
compareReplicateSDPerScreen	0.311	0.023	0.334
compareReplicates	0.214	0.035	0.276
controlDensity	0.055	0.008	0.068
controlDensityPerPlate	0.194	0.025	0.231
controlDensityPerScreen	0.094	0.014	0.117
controlNorm	0.008	0.000	0.009
createSubset	0.001	0.000	0.002
discardLabtek	0.003	0.000	0.002
discardWells	0.003	0.000	0.003
divNorm	0.008	0.001	0.009
divideChannels	0.002	0.000	0.002
eraseDataSetColumn	0.006	0.000	0.007
findReplicates	0.002	0.001	0.003
furthestFromZero	0.002	0.000	0.002
generateDatasetFile	0.010	0.001	0.010
generateRepMatNoFilter	0.003	0.001	0.004
generateReplicateMat	0.006	0.000	0.006
gseaAnalysis	5.272	0.134	14.712
hitselectionPval	0.021	0.001	0.022
hitselectionZscore	0.030	0.001	0.031
hitselectionZscorePval	0.026	0.001	0.027
incorporatepValVec	0.015	0.001	0.017
indexSubset	0.002	0.000	0.002
joinDatasetFiles	0.263	0.003	0.273
joinDatasets	0.003	0.000	0.005
lowessNorm	0.008	0.001	0.009
mainAnalysis	24.041	2.671	28.023
makeBoxplot4PlateType	0.065	0.010	0.080
makeBoxplotControls	0.036	0.005	0.053
makeBoxplotControlsPerPlate	0.136	0.015	0.157
makeBoxplotControlsPerScreen	0.063	0.008	0.074
makeBoxplotPerPlate	0.058	0.008	0.068
makeBoxplotPerScreen	0.031	0.005	0.036
multTestAdjust	0.003	0.001	0.003
numCellQualControl	0.040	0.004	0.045
orderGeneIDs	0.044	0.001	0.045
percCellQualControl	0.024	0.003	0.027
plotBar	0.129	0.010	0.147
plotControlHisto	0.082	0.006	0.090
plotControlHistoPerplate	0.371	0.021	0.418
plotControlHistoPerscreen	0.182	0.011	0.200
plotHisto	0.029	0.006	0.036
plotHistoPerplate	0.124	0.019	0.152
plotHistoPerscreen	0.057	0.009	0.070
plotQQ	0.033	0.005	0.040
plotQQperplate	0.104	0.017	0.128
plotQQperscreen	0.063	0.008	0.075
quantileNormalization	0.021	0.001	0.023
replicatesCV	0.063	0.010	0.077
replicatesSpearmancor	0.022	0.002	0.025
rms	0.002	0.000	0.003
rnaither	15.323	1.625	18.564
saveDataset	0.017	0.001	0.018
saveOldIntensityColumns	0.003	0.001	0.003
savepValVec	0.004	0.001	0.004
spatialDistrib	0.609	0.050	0.669
spatialDistribHits	0.613	0.050	0.676
subtractBackground	0.003	0.000	0.004
sumChannels	0.010	0.001	0.010
summarizeReps	0.051	0.001	0.052
summarizeRepsNoFiltering	0.066	0.001	0.067
trim	0.004	0.001	0.004
varAdjust	0.005	0.001	0.006
vennDiag	0.073	0.010	0.081
volcanoPlot	0.059	0.007	0.067

CHECK report for RNAither on merida1

Summary

Command output

Installation output

Tests output

Example timings