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This page was generated on 2023-04-12 11:05:45 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


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 1475/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.34.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_16
git_last_commit: d0f8883
git_last_commit_date: 2022-11-01 11:09:03 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhenStat
Version: 2.34.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PhenStat_2.34.0.tar.gz
StartedAt: 2023-04-11 04:29:28 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 04:31:47 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 139.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PhenStat_2.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/PhenStat.Rcheck'
* using R version 4.2.3 (2023-03-15 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 '2.34.0'
* 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-3.16-bioc/meat/PhenStat.Rcheck/00check.log'
for details.



Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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 -- Tue Apr 11 04:31:33 2023 
*********************************************** 
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 
   2.81    0.43    3.21 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.150.000.17
JSONOutput0.940.020.95
LRDataset0.060.000.07
PhenList-class0.250.010.26
PhenList0.190.040.22
PhenStatReport0.030.000.03
PhenTestResult-class0.750.010.77
PhenTestResult0.670.000.67
RRTest0.080.000.08
TFDataset0.160.020.17
analysedDataset0.720.040.77
analysisResults0.730.020.75
boxplotResidualBatch1.060.031.09
boxplotSexGenotype0.100.000.09
boxplotSexGenotypeBatch0.150.000.16
boxplotSexGenotypeBatchAdjusted0.070.000.06
boxplotSexGenotypeResult0.980.000.99
boxplotSexGenotypeWeightBatchAdjusted0.060.000.06
categoricalBarplot0.110.000.11
checkDataset0.050.000.05
classificationTag0.780.000.78
determiningLambda1.020.371.39
dim0.030.000.03
finalLRModel0.530.020.57
finalModel0.660.000.65
finalTFModel0.360.000.36
htestPhenStat-class0.100.000.11
modelFormula000
modelFormulaLR000
parserOutputSummary0.880.000.88
parserOutputSummaryLR0.560.000.56
parserOutputTFSummary0.080.000.08
performReverseTransformation000
performTransformation000
plot.PhenList3.280.123.41
plot.PhenTestResult2.280.062.34
plotResidualPredicted0.730.000.74
printLROutput0.50.00.5
printTabStyle000
qqplotGenotype0.780.000.78
qqplotRandomEffects1.050.001.05
qqplotRotatedResiduals3.310.043.34
recommendMethod0.160.010.17
scatterplotGenotypeWeight0.120.000.13
scatterplotGenotypeWeightResult0.970.000.97
scatterplotSexGenotypeBatch0.080.000.08
scatterplotSexGenotypeBatchResult0.930.000.94
startLRModel0.520.020.53
startModel0.670.000.67
startTFModel0.330.000.33
summaryOutput0.830.010.84
summaryPhenListResult0.830.030.86
testDataset2.560.032.61
testFinalLRModel0.510.000.52
testFinalModel0.860.020.87
vectorOutput0.830.030.86
vectorOutputMatrices0.130.000.12