Multiple platform build/check report for BioC 3.11 - CHECK report for RNAither on machv2

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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_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/RNAither.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.36.0’
* 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 ... 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 (user + system) or elapsed time > 5s
               user system elapsed
mainAnalysis 19.389  4.288  38.252
rnaither     16.787  4.399  29.013
gseaAnalysis 10.763  0.193  12.656
* 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-3.11-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.
** 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.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (RNAither)

Tests output

Example timings

name	user	system	elapsed
BScore	0.046	0.001	0.047
DRQualControl	0.048	0.004	0.052
LiWongRank	0.098	0.004	0.102
MannWhitney	0.037	0.002	0.038
RankProduct	0.147	0.006	0.154
SNRQualControl	0.024	0.007	0.030
Ttest	0.029	0.002	0.031
ZPRIMEQualControl	0.040	0.012	0.074
ZScore	0.014	0.002	0.016
ZScorePerScreen	0.008	0.002	0.010
ZScorePlot	0.042	0.011	0.081
ZScorePlotTwo	0.024	0.007	0.047
channelPlot	0.025	0.008	0.050
closestToZero	0.002	0.001	0.004
compareHits	0.058	0.004	0.102
compareReplicaPlates	0.016	0.003	0.019
compareReplicateSD	0.146	0.020	0.262
compareReplicateSDPerScreen	0.252	0.037	0.482
compareReplicates	0.121	0.020	0.173
controlDensity	0.048	0.011	0.091
controlDensityPerPlate	0.153	0.019	0.209
controlDensityPerScreen	0.073	0.020	0.164
controlNorm	0.012	0.002	0.014
createSubset	0.003	0.001	0.004
discardLabtek	0.003	0.001	0.004
discardWells	0.004	0.001	0.005
divNorm	0.014	0.001	0.016
divideChannels	0.002	0.001	0.003
eraseDataSetColumn	0.011	0.001	0.012
findReplicates	0.004	0.001	0.005
furthestFromZero	0.002	0.000	0.003
generateDatasetFile	0.014	0.002	0.016
generateRepMatNoFilter	0.006	0.001	0.007
generateReplicateMat	0.009	0.001	0.009
gseaAnalysis	10.763	0.193	12.656
hitselectionPval	0.016	0.002	0.018
hitselectionZscore	0.019	0.001	0.021
hitselectionZscorePval	0.018	0.002	0.020
incorporatepValVec	0.012	0.002	0.013
indexSubset	0.002	0.001	0.002
joinDatasetFiles	0.012	0.002	0.015
joinDatasets	0.002	0.000	0.003
lowessNorm	0.008	0.001	0.009
mainAnalysis	19.389	4.288	38.252
makeBoxplot4PlateType	0.073	0.015	0.122
makeBoxplotControls	0.029	0.009	0.067
makeBoxplotControlsPerPlate	0.108	0.019	0.166
makeBoxplotControlsPerScreen	0.055	0.010	0.085
makeBoxplotPerPlate	0.052	0.009	0.080
makeBoxplotPerScreen	0.028	0.008	0.054
multTestAdjust	0.002	0.001	0.002
numCellQualControl	0.025	0.005	0.031
orderGeneIDs	0.055	0.001	0.056
percCellQualControl	0.025	0.005	0.030
plotBar	0.137	0.043	0.221
plotControlHisto	0.086	0.015	0.130
plotControlHistoPerplate	0.394	0.061	0.551
plotControlHistoPerscreen	0.182	0.030	0.266
plotHisto	0.016	0.007	0.040
plotHistoPerplate	0.072	0.014	0.120
plotHistoPerscreen	0.036	0.007	0.067
plotQQ	0.023	0.007	0.046
plotQQperplate	0.079	0.017	0.129
plotQQperscreen	0.042	0.008	0.067
quantileNormalization	0.019	0.001	0.020
replicatesCV	0.042	0.006	0.071
replicatesSpearmancor	0.019	0.003	0.023
rms	0.003	0.001	0.004
rnaither	16.787	4.399	29.013
saveDataset	0.015	0.003	0.018
saveOldIntensityColumns	0.003	0.001	0.004
savepValVec	0.003	0.001	0.005
spatialDistrib	0.382	0.065	0.846
spatialDistribHits	0.424	0.068	0.899
subtractBackground	0.005	0.002	0.006
sumChannels	0.014	0.001	0.015
summarizeReps	0.029	0.001	0.029
summarizeRepsNoFiltering	0.027	0.001	0.029
trim	0.002	0.001	0.003
varAdjust	0.006	0.001	0.007
vennDiag	0.075	0.009	0.095
volcanoPlot	0.052	0.007	0.077

CHECK report for RNAither on machv2

Summary

Command output

Installation output

Tests output

Example timings