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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).

CHECK results for PhenStat on machv2

To the developers/maintainers of the PhenStat package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhenStat.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1383/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.28.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_13
git_last_commit: d1496a6
git_last_commit_date: 2021-05-19 12:02:09 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhenStat
Version: 2.28.0
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_2.28.0.tar.gz
StartedAt: 2021-10-14 22:17:44 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:20:49 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 184.4 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_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PhenStat.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.28.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
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 Oct 14 22:20:34 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 
  4.537   0.313   4.834 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.2130.0220.236
JSONOutput1.2640.0381.321
LRDataset0.0720.0080.078
PhenList-class0.2660.0190.286
PhenList0.2580.0070.266
PhenStatReport0.0520.0020.054
PhenTestResult-class1.1710.0251.202
PhenTestResult0.8710.0100.882
RRTest0.1530.0050.158
TFDataset0.4530.0090.464
analysedDataset1.0260.0141.041
analysisResults1.0730.0191.124
boxplotResidualBatch1.1780.0221.200
boxplotSexGenotype0.1270.0060.136
boxplotSexGenotypeBatch0.2340.0060.241
boxplotSexGenotypeBatchAdjusted0.1110.0020.113
boxplotSexGenotypeResult1.3450.0151.479
boxplotSexGenotypeWeightBatchAdjusted0.0710.0010.072
categoricalBarplot0.2330.0080.243
checkDataset0.0550.0020.057
classificationTag1.1160.0101.134
determiningLambda1.0290.3731.403
dim0.0560.0010.057
finalLRModel0.6980.0080.706
finalModel0.9600.0080.970
finalTFModel0.8360.0230.883
htestPhenStat-class0.2100.0090.220
modelFormula0.0000.0000.001
modelFormulaLR0.0000.0010.000
parserOutputSummary1.2010.0121.214
parserOutputSummaryLR0.5930.0060.599
parserOutputTFSummary0.1540.0020.156
performReverseTransformation0.0000.0010.001
performTransformation0.0000.0000.001
plot.PhenList3.0380.0713.136
plot.PhenTestResult3.1580.0793.260
plotResidualPredicted1.0110.0061.019
printLROutput0.6550.0140.670
printTabStyle0.0010.0010.002
qqplotGenotype1.0900.0051.098
qqplotRandomEffects1.0280.0211.050
qqplotRotatedResiduals4.5680.0744.688
recommendMethod0.4040.0070.411
scatterplotGenotypeWeight0.2160.0050.222
scatterplotGenotypeWeightResult1.2030.0141.219
scatterplotSexGenotypeBatch0.1200.0040.125
scatterplotSexGenotypeBatchResult1.3310.0101.342
startLRModel0.7930.0100.810
startModel0.8510.0030.858
startTFModel0.7010.0070.709
summaryOutput1.1090.0221.132
summaryPhenListResult1.1920.0131.206
testDataset3.0530.0553.118
testFinalLRModel0.5240.0070.531
testFinalModel1.1810.0061.189
vectorOutput1.1890.0291.220
vectorOutputMatrices0.1970.0190.217