Multiple platform build/check report for BioC 3.7 - CHECK report for RNAither on merida2

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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_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RNAither.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.28.0’
* 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 or elapsed time > 5s
               user system elapsed
mainAnalysis 23.241  2.653  27.142
rnaither     15.878  1.647  19.121
gseaAnalysis  5.178  0.132  10.163
* 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-3.7-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	0.047	0.001	0.048
DRQualControl	0.026	0.003	0.028
LiWongRank	0.097	0.002	0.102
MannWhitney	0.045	0.001	0.046
RankProduct	0.129	0.006	0.137
SNRQualControl	0.044	0.008	0.051
Ttest	0.030	0.000	0.031
ZPRIMEQualControl	0.043	0.012	0.057
ZScore	0.016	0.001	0.015
ZScorePerScreen	0.011	0.001	0.012
ZScorePlot	0.107	0.029	0.149
ZScorePlotTwo	0.028	0.022	0.035
channelPlot	0.035	0.005	0.042
closestToZero	0.003	0.001	0.003
compareHits	0.041	0.002	0.044
compareReplicaPlates	0.015	0.002	0.017
compareReplicateSD	0.199	0.013	0.218
compareReplicateSDPerScreen	0.349	0.022	0.374
compareReplicates	0.218	0.034	0.281
controlDensity	0.059	0.008	0.071
controlDensityPerPlate	0.205	0.024	0.244
controlDensityPerScreen	0.109	0.015	0.136
controlNorm	0.015	0.001	0.016
createSubset	0.004	0.000	0.005
discardLabtek	0.005	0.000	0.005
discardWells	0.003	0.001	0.004
divNorm	0.013	0.000	0.013
divideChannels	0.004	0.000	0.004
eraseDataSetColumn	0.012	0.000	0.013
findReplicates	0.004	0.000	0.005
furthestFromZero	0.004	0.000	0.004
generateDatasetFile	0.021	0.002	0.022
generateRepMatNoFilter	0.008	0.001	0.008
generateReplicateMat	0.008	0.000	0.008
gseaAnalysis	5.178	0.132	10.163
hitselectionPval	0.024	0.001	0.026
hitselectionZscore	0.031	0.001	0.031
hitselectionZscorePval	0.032	0.002	0.034
incorporatepValVec	0.019	0.001	0.021
indexSubset	0.003	0.001	0.004
joinDatasetFiles	0.259	0.005	0.268
joinDatasets	0.005	0.001	0.005
lowessNorm	0.012	0.001	0.014
mainAnalysis	23.241	2.653	27.142
makeBoxplot4PlateType	0.061	0.008	0.073
makeBoxplotControls	0.034	0.004	0.039
makeBoxplotControlsPerPlate	0.126	0.015	0.145
makeBoxplotControlsPerScreen	0.068	0.008	0.078
makeBoxplotPerPlate	0.068	0.008	0.076
makeBoxplotPerScreen	0.032	0.005	0.038
multTestAdjust	0.002	0.001	0.003
numCellQualControl	0.033	0.002	0.036
orderGeneIDs	0.040	0.000	0.042
percCellQualControl	0.027	0.002	0.036
plotBar	0.150	0.010	0.169
plotControlHisto	0.093	0.006	0.101
plotControlHistoPerplate	0.370	0.022	0.406
plotControlHistoPerscreen	0.175	0.011	0.190
plotHisto	0.028	0.005	0.035
plotHistoPerplate	0.114	0.016	0.139
plotHistoPerscreen	0.054	0.008	0.078
plotQQ	0.035	0.005	0.065
plotQQperplate	0.106	0.017	0.127
plotQQperscreen	0.055	0.008	0.065
quantileNormalization	0.017	0.000	0.017
replicatesCV	0.062	0.009	0.073
replicatesSpearmancor	0.020	0.002	0.021
rms	0.003	0.000	0.003
rnaither	15.878	1.647	19.121
saveDataset	0.013	0.001	0.014
saveOldIntensityColumns	0.003	0.001	0.003
savepValVec	0.003	0.000	0.004
spatialDistrib	0.551	0.049	0.626
spatialDistribHits	0.629	0.051	0.695
subtractBackground	0.004	0.000	0.005
sumChannels	0.014	0.001	0.016
summarizeReps	0.061	0.001	0.062
summarizeRepsNoFiltering	0.056	0.001	0.058
trim	0.004	0.000	0.005
varAdjust	0.006	0.001	0.008
vennDiag	0.073	0.010	0.083
volcanoPlot	0.061	0.009	0.069

CHECK report for RNAither on merida2

Summary

Command output

Installation output

Tests output

Example timings