Multiple platform build/check report for BioC 3.8 - CHECK report for PhenStat 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:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhenStat_2.18.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/PhenStat.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 ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.18.1’
* 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 ‘PhenStat’ 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 ... OK
* 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
Namespace in Imports field not imported from: ‘SmoothWin’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/PhenStat.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 PhenStat
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘PhenStat’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PhenStat)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("PhenStat")

 >=========================================================================<
 This version of PhenStat includes *FEWER* functions than the previous ones 
 You *still* can use the previous functions by using `:::`. For example :   
 PhenStat:::boxplotSexGenotype   or   PhenStat:::FisherExactTest            
 *** Want to know what is new in this version? run PhenStat:::WhatIsNew()   
 >=========================================================================<


RUNIT TEST PROTOCOL -- Tue Apr 16 01:56:01 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.805   0.303   4.103

Example timings

name	user	system	elapsed
FisherExactTest	0.273	0.022	0.298
JSONOutput	1.251	0.040	1.305
LRDataset	0.111	0.007	0.117
PhenList-class	0.233	0.006	0.239
PhenList	0.253	0.004	0.259
PhenStatReport	0.074	0.001	0.076
PhenTestResult-class	1.039	0.017	1.062
PhenTestResult	0.764	0.013	0.778
RRTest	0.164	0.006	0.170
TFDataset	0.518	0.005	0.529
analysedDataset	0.927	0.011	0.942
analysisResults	0.852	0.009	0.864
boxplotResidualBatch	1.003	0.006	1.016
boxplotSexGenotype	0.093	0.002	0.096
boxplotSexGenotypeBatch	0.198	0.004	0.203
boxplotSexGenotypeBatchAdjusted	0.112	0.003	0.115
boxplotSexGenotypeResult	1.141	0.028	1.186
boxplotSexGenotypeWeightBatchAdjusted	0.120	0.010	0.132
categoricalBarplot	0.258	0.003	0.263
checkDataset	0.067	0.001	0.068
classificationTag	1.156	0.009	1.188
determiningLambda	0.713	0.253	0.988
dim	0.047	0.001	0.049
finalLRModel	0.665	0.010	0.685
finalModel	0.724	0.013	0.745
finalTFModel	0.829	0.009	0.846
htestPhenStat-class	0.259	0.009	0.274
modelFormula	0.001	0.001	0.000
modelFormulaLR	0	0	0
parserOutputSummary	0.842	0.010	0.868
parserOutputSummaryLR	0.860	0.006	0.878
parserOutputTFSummary	0.130	0.001	0.146
performReverseTransformation	0.001	0.000	0.000
performTransformation	0.000	0.000	0.001
plot.PhenList	2.805	0.034	2.887
plot.PhenTestResult	2.743	0.028	2.805
plotResidualPredicted	0.995	0.008	1.009
printLROutput	0.608	0.012	0.621
printTabStyle	0.004	0.001	0.005
qqplotGenotype	0.938	0.004	0.945
qqplotRandomEffects	0.841	0.002	0.846
qqplotRotatedResiduals	4.580	0.045	4.642
recommendMethod	0.421	0.003	0.424
scatterplotGenotypeWeight	0.145	0.003	0.149
scatterplotGenotypeWeightResult	1.222	0.014	1.241
scatterplotSexGenotypeBatch	0.109	0.002	0.114
scatterplotSexGenotypeBatchResult	1.124	0.007	1.135
startLRModel	0.676	0.019	0.696
startModel	0.622	0.002	0.625
startTFModel	0.742	0.006	0.750
summaryOutput	1.134	0.010	1.149
summaryPhenListResult	1.097	0.011	1.112
testDataset	2.586	0.028	2.624
testFinalLRModel	0.629	0.011	0.640
testFinalModel	1.032	0.009	1.043
vectorOutput	1.289	0.014	1.309
vectorOutputMatrices	0.262	0.004	0.268

CHECK report for PhenStat on merida1

Summary

Command output

Installation output

Tests output

Example timings