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

This page was generated on 2021-06-18 14:06:54 -0400 (Fri, 18 Jun 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: 2021-06-17 06:50:12 -0400 (Thu, 17 Jun 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: 2021-06-17 22:04:00 -0400 (Thu, 17 Jun 2021)
EndedAt: 2021-06-17 22:06:59 -0400 (Thu, 17 Jun 2021)
EllapsedTime: 178.5 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 Jun 17 22:06:48 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 
  4.142   0.277   4.411 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.2640.0280.293
JSONOutput1.2940.0381.333
LRDataset0.0740.0050.080
PhenList-class0.2930.0120.306
PhenList0.2500.0090.261
PhenStatReport0.0570.0020.060
PhenTestResult-class0.9500.0190.971
PhenTestResult0.8850.0120.898
RRTest0.1410.0030.145
TFDataset0.4270.0050.433
analysedDataset1.0290.0121.044
analysisResults0.9360.0090.945
boxplotResidualBatch1.3580.0181.377
boxplotSexGenotype0.1080.0050.114
boxplotSexGenotypeBatch0.1810.0060.187
boxplotSexGenotypeBatchAdjusted0.0940.0010.097
boxplotSexGenotypeResult1.3720.0161.390
boxplotSexGenotypeWeightBatchAdjusted0.0920.0020.095
categoricalBarplot0.2060.0100.216
checkDataset0.0710.0020.074
classificationTag1.0150.0101.026
determiningLambda0.8990.2621.161
dim0.0420.0010.043
finalLRModel0.6580.0060.664
finalModel0.6750.0090.683
finalTFModel0.8970.0100.908
htestPhenStat-class0.1760.0050.182
modelFormula0.0000.0000.001
modelFormulaLR0.0000.0010.000
parserOutputSummary0.8520.0130.865
parserOutputSummaryLR0.5930.0090.602
parserOutputTFSummary0.1510.0020.153
performReverseTransformation0.0000.0000.001
performTransformation0.0000.0000.001
plot.PhenList3.1320.0753.218
plot.PhenTestResult2.8120.0472.879
plotResidualPredicted0.9760.0060.984
printLROutput0.7330.0110.747
printTabStyle0.0010.0010.002
qqplotGenotype1.0450.0161.084
qqplotRandomEffects1.0160.0081.025
qqplotRotatedResiduals4.1250.0464.183
recommendMethod0.6930.0090.701
scatterplotGenotypeWeight0.1980.0090.207
scatterplotGenotypeWeightResult1.2270.0151.244
scatterplotSexGenotypeBatch0.1090.0040.115
scatterplotSexGenotypeBatchResult1.4330.0121.470
startLRModel0.5500.0040.555
startModel0.8500.0060.857
startTFModel0.6580.0060.664
summaryOutput1.2730.0111.284
summaryPhenListResult1.1160.0091.125
testDataset2.7870.0532.940
testFinalLRModel0.4880.0070.495
testFinalModel1.0610.0221.085
vectorOutput1.1180.0151.133
vectorOutputMatrices0.2010.0040.213