Multiple platform build/check report for BioC 3.12 - 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_2.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/RNAither.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.38.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'prada' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/RNAither.Rcheck/00install.out’ for details.
* 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 (user + system) or elapsed time > 5s
               user system elapsed
mainAnalysis 14.667  1.259  16.787
gseaAnalysis 14.646  0.899  17.755
rnaither      9.969  0.485  10.473
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-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/4.0/Resources/library’
* installing *source* package ‘RNAither’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning message:
Package 'prada' is deprecated and will be removed from Bioconductor
  version 3.13 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (RNAither)

Tests output

Example timings

name	user	system	elapsed
BScore	0.031	0.001	0.032
DRQualControl	0.024	0.004	0.028
LiWongRank	0.083	0.002	0.085
MannWhitney	0.033	0.002	0.034
RankProduct	0.166	0.004	0.171
SNRQualControl	0.024	0.007	0.032
Ttest	0.031	0.002	0.032
ZPRIMEQualControl	0.067	0.019	0.093
ZScore	0.016	0.002	0.017
ZScorePerScreen	0.010	0.001	0.012
ZScorePlot	0.050	0.005	0.056
ZScorePlotTwo	0.027	0.004	0.030
channelPlot	0.024	0.003	0.028
closestToZero	0.001	0.001	0.002
compareHits	0.055	0.004	0.059
compareReplicaPlates	0.019	0.004	0.023
compareReplicateSD	0.144	0.005	0.149
compareReplicateSDPerScreen	0.162	0.005	0.167
compareReplicates	0.108	0.007	0.115
controlDensity	0.035	0.004	0.039
controlDensityPerPlate	0.145	0.009	0.154
controlDensityPerScreen	0.059	0.006	0.066
controlNorm	0.013	0.001	0.014
createSubset	0.002	0.000	0.002
discardLabtek	0.003	0.000	0.004
discardWells	0.003	0.001	0.004
divNorm	0.030	0.002	0.031
divideChannels	0.003	0.001	0.003
eraseDataSetColumn	0.008	0.001	0.009
findReplicates	0.004	0.002	0.005
furthestFromZero	0.001	0.001	0.002
generateDatasetFile	0.013	0.002	0.015
generateRepMatNoFilter	0.004	0.000	0.004
generateReplicateMat	0.009	0.001	0.010
gseaAnalysis	14.646	0.899	17.755
hitselectionPval	0.022	0.002	0.024
hitselectionZscore	0.019	0.002	0.020
hitselectionZscorePval	0.018	0.002	0.019
incorporatepValVec	0.014	0.001	0.015
indexSubset	0.003	0.001	0.004
joinDatasetFiles	0.014	0.003	0.017
joinDatasets	0.003	0.001	0.004
lowessNorm	0.009	0.002	0.012
mainAnalysis	14.667	1.259	16.787
makeBoxplot4PlateType	0.038	0.005	0.043
makeBoxplotControls	0.019	0.003	0.022
makeBoxplotControlsPerPlate	0.080	0.005	0.085
makeBoxplotControlsPerScreen	0.040	0.004	0.044
makeBoxplotPerPlate	0.032	0.003	0.035
makeBoxplotPerScreen	0.018	0.002	0.021
multTestAdjust	0.002	0.001	0.003
numCellQualControl	0.021	0.005	0.026
orderGeneIDs	0.062	0.002	0.064
percCellQualControl	0.022	0.005	0.027
plotBar	0.094	0.003	0.099
plotControlHisto	0.069	0.003	0.074
plotControlHistoPerplate	0.275	0.006	0.282
plotControlHistoPerscreen	0.143	0.004	0.147
plotHisto	0.015	0.002	0.016
plotHistoPerplate	0.059	0.005	0.064
plotHistoPerscreen	0.025	0.002	0.027
plotQQ	0.017	0.002	0.019
plotQQperplate	0.067	0.005	0.073
plotQQperscreen	0.039	0.003	0.042
quantileNormalization	0.016	0.002	0.017
replicatesCV	0.037	0.003	0.040
replicatesSpearmancor	0.015	0.003	0.018
rms	0.001	0.001	0.003
rnaither	9.969	0.485	10.473
saveDataset	0.011	0.002	0.013
saveOldIntensityColumns	0.003	0.001	0.004
savepValVec	0.004	0.002	0.005
spatialDistrib	0.287	0.012	0.300
spatialDistribHits	0.338	0.015	0.402
subtractBackground	0.005	0.002	0.008
sumChannels	0.014	0.002	0.017
summarizeReps	0.044	0.001	0.046
summarizeRepsNoFiltering	0.034	0.001	0.035
trim	0.004	0.001	0.006
varAdjust	0.009	0.002	0.010
vennDiag	0.067	0.006	0.073
volcanoPlot	0.049	0.004	0.053

CHECK report for RNAither on merida1

Summary

Command output

Installation output

Tests output

Example timings