Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2021-07-30 15:06:34 -0400 (Fri, 30 Jul 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: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/PhenStat
Branch: RELEASE_3_13
Last Commit: d1496a6
Last Changed 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: 2021-07-29 21:57:12 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 22:00:12 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 179.7 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.1.0 (2021-05-18)
* 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

##############################################################################
##############################################################################
###
### 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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 Jul 29 22:00:01 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 
  4.872   0.304   5.155 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.2320.0200.252
JSONOutput1.1840.0411.226
LRDataset0.0950.0070.102
PhenList-class0.2900.0140.304
PhenList0.2560.0080.264
PhenStatReport0.0570.0020.059
PhenTestResult-class1.1560.0301.186
PhenTestResult0.8200.0170.838
RRTest0.1360.0040.140
TFDataset0.4590.0100.469
analysedDataset1.0680.0091.076
analysisResults0.9060.0090.916
boxplotResidualBatch1.0930.0211.118
boxplotSexGenotype0.1320.0060.138
boxplotSexGenotypeBatch0.2030.0050.208
boxplotSexGenotypeBatchAdjusted0.0920.0020.095
boxplotSexGenotypeResult1.2680.0121.285
boxplotSexGenotypeWeightBatchAdjusted0.1020.0020.105
categoricalBarplot0.2520.0090.262
checkDataset0.0610.0010.061
classificationTag1.0530.0071.063
determiningLambda1.1310.3421.475
dim0.0560.0010.057
finalLRModel0.5930.0080.602
finalModel0.8180.0210.845
finalTFModel0.7490.0160.766
htestPhenStat-class0.2210.0090.230
modelFormula0.0010.0000.000
modelFormulaLR0.0000.0000.001
parserOutputSummary1.0660.0051.072
parserOutputSummaryLR0.5400.0070.547
parserOutputTFSummary0.1460.0010.147
performReverseTransformation000
performTransformation000
plot.PhenList3.2440.0653.314
plot.PhenTestResult3.1120.0603.181
plotResidualPredicted0.9500.0100.961
printLROutput0.5480.0050.553
printTabStyle0.0010.0000.002
qqplotGenotype0.9530.0160.970
qqplotRandomEffects1.0170.0121.030
qqplotRotatedResiduals4.5170.0444.616
recommendMethod0.4560.0120.469
scatterplotGenotypeWeight0.2160.0070.226
scatterplotGenotypeWeightResult1.5230.0081.534
scatterplotSexGenotypeBatch0.1240.0040.129
scatterplotSexGenotypeBatchResult1.3090.0111.323
startLRModel0.6610.0130.674
startModel0.9520.0030.957
startTFModel0.8310.0090.840
summaryOutput1.1830.0111.195
summaryPhenListResult1.2770.0161.294
testDataset3.1920.0543.251
testFinalLRModel0.7500.0080.759
testFinalModel1.0790.0101.090
vectorOutput1.0240.0121.036
vectorOutputMatrices0.1370.0080.144