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CHECK report for PhenStat on merida1

This page was generated on 2021-05-06 12:36:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PhenStat package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1339/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.26.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PhenStat
Branch: RELEASE_3_12
Last Commit: 65ed760
Last Changed Date: 2020-10-27 10:54:09 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: PhenStat
Version: 2.26.0
Command: /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_2.26.0.tar.gz
StartedAt: 2021-05-06 04:39:49 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:43:05 -0400 (Thu, 06 May 2021)
EllapsedTime: 195.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /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_2.26.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/PhenStat.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 ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.26.0’
* 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 ‘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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.154  0.041   5.201
* 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-3.12-bioc/meat/PhenStat.Rcheck/00check.log’
for details.



Installation output

PhenStat.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PhenStat’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PhenStat)

Tests output

PhenStat.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 -- Thu May  6 04:42:55 2021 
*********************************************** 
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 
  4.549   0.338   4.869 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.2410.0220.263
JSONOutput1.7000.0371.740
LRDataset0.0710.0020.074
PhenList-class0.3160.0170.335
PhenList0.2700.0070.278
PhenStatReport0.0590.0010.062
PhenTestResult-class1.5320.0141.548
PhenTestResult1.2440.0101.254
RRTest0.1230.0040.126
TFDataset0.4540.0070.462
analysedDataset1.5500.0111.587
analysisResults1.5960.0161.613
boxplotResidualBatch1.5030.0171.521
boxplotSexGenotype0.1140.0050.118
boxplotSexGenotypeBatch0.2190.0050.225
boxplotSexGenotypeBatchAdjusted0.0980.0050.103
boxplotSexGenotypeResult1.8100.0211.839
boxplotSexGenotypeWeightBatchAdjusted0.0960.0020.098
categoricalBarplot0.1980.0040.203
checkDataset0.0640.0010.065
classificationTag1.5080.0151.525
determiningLambda0.8850.2121.099
dim0.0530.0020.055
finalLRModel0.6920.0090.702
finalModel1.0860.0031.089
finalTFModel0.8120.0110.824
htestPhenStat-class0.2030.0040.208
modelFormula0.0010.0000.000
modelFormulaLR0.0010.0000.001
parserOutputSummary1.3340.0071.342
parserOutputSummaryLR0.6120.0130.626
parserOutputTFSummary0.1690.0020.171
performReverseTransformation0.0010.0000.001
performTransformation0.0000.0000.001
plot.PhenList3.7860.0613.853
plot.PhenTestResult3.7540.0673.874
plotResidualPredicted1.4060.0131.422
printLROutput0.4520.0100.463
printTabStyle0.0010.0010.002
qqplotGenotype1.3980.0161.415
qqplotRandomEffects1.2280.0101.240
qqplotRotatedResiduals5.1540.0415.201
recommendMethod0.3090.0020.310
scatterplotGenotypeWeight0.1940.0080.204
scatterplotGenotypeWeightResult1.7690.0121.785
scatterplotSexGenotypeBatch0.1220.0060.130
scatterplotSexGenotypeBatchResult1.4590.0131.474
startLRModel0.5020.0080.511
startModel1.3990.0051.406
startTFModel0.7390.0080.748
summaryOutput1.4150.0191.435
summaryPhenListResult1.3350.0221.362
testDataset3.5130.0573.580
testFinalLRModel0.5710.0070.581
testFinalModel1.5130.0121.531
vectorOutput1.4320.0191.458
vectorOutputMatrices0.1910.0040.195