Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:01 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for PhenStat on palomino3


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? 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 1447/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.32.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_15
git_last_commit: 2e144f6
git_last_commit_date: 2022-04-26 11:17:16 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhenStat
Version: 2.32.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PhenStat_2.32.0.tar.gz
StartedAt: 2022-10-19 02:50:42 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:53:22 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 160.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PhenStat_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/PhenStat.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '2.32.0'
* 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 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
  'F:/biocbuild/bbs-3.15-bioc/meat/PhenStat.Rcheck/00check.log'
for details.



Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Wed Oct 19 02:53:09 2022 
*********************************************** 
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 
   3.46    0.42    3.84 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.220.011.00
JSONOutput1.390.021.42
LRDataset0.080.000.31
PhenList-class0.170.030.77
PhenList0.150.010.17
PhenStatReport0.030.000.03
PhenTestResult-class0.770.000.77
PhenTestResult0.910.020.92
RRTest0.150.020.17
TFDataset0.320.010.33
analysedDataset0.900.030.93
analysisResults0.750.000.75
boxplotResidualBatch0.80.00.8
boxplotSexGenotype0.060.000.06
boxplotSexGenotypeBatch0.160.010.17
boxplotSexGenotypeBatchAdjusted0.080.000.08
boxplotSexGenotypeResult1.370.001.37
boxplotSexGenotypeWeightBatchAdjusted0.090.000.10
categoricalBarplot0.470.030.50
checkDataset0.070.000.06
classificationTag0.790.040.82
determiningLambda1.390.401.80
dim0.050.000.05
finalLRModel0.640.020.68
finalModel0.620.010.64
finalTFModel0.360.000.37
htestPhenStat-class0.110.000.11
modelFormula000
modelFormulaLR000
parserOutputSummary0.730.000.74
parserOutputSummaryLR0.550.000.54
parserOutputTFSummary0.090.000.10
performReverseTransformation000
performTransformation000
plot.PhenList2.880.103.00
plot.PhenTestResult2.970.063.03
plotResidualPredicted0.950.020.97
printLROutput0.990.000.98
printTabStyle000
qqplotGenotype0.900.010.92
qqplotRandomEffects0.770.000.77
qqplotRotatedResiduals3.810.033.84
recommendMethod0.280.020.30
scatterplotGenotypeWeight0.160.000.15
scatterplotGenotypeWeightResult1.310.001.35
scatterplotSexGenotypeBatch0.090.000.09
scatterplotSexGenotypeBatchResult1.320.001.33
startLRModel0.450.010.47
startModel0.890.000.89
startTFModel0.450.000.45
summaryOutput1.210.031.24
summaryPhenListResult0.860.000.86
testDataset2.730.103.00
testFinalLRModel0.550.000.54
testFinalModel1.030.011.05
vectorOutput1.030.001.03
vectorOutputMatrices0.110.000.11