Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-06-24 11:05:39 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 nebbiolo2


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 1432/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.33.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: master
git_last_commit: bc50b05
git_last_commit_date: 2022-04-26 11:17:16 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhenStat
Version: 2.33.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings PhenStat_2.33.0.tar.gz
StartedAt: 2022-06-23 21:11:19 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:13:12 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 112.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings PhenStat_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/PhenStat.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (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 ‘2.33.0’
* 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 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 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
  ‘/home/biocbuild/bbs-3.16-bioc/meat/PhenStat.Rcheck/00check.log’
for details.



Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library ‘/home/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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 23 21:13:07 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 
  3.111   0.190   3.282 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.1250.0160.141
JSONOutput0.750.000.75
LRDataset0.0420.0000.043
PhenList-class0.1740.0000.175
PhenList0.1860.0000.186
PhenStatReport0.0330.0000.033
PhenTestResult-class0.6040.0040.608
PhenTestResult0.4950.0080.503
RRTest0.0780.0040.082
TFDataset0.2090.0520.261
analysedDataset0.6040.0040.608
analysisResults0.6000.0120.612
boxplotResidualBatch0.6640.0000.664
boxplotSexGenotype0.0650.0000.065
boxplotSexGenotypeBatch0.1260.0000.126
boxplotSexGenotypeBatchAdjusted0.0610.0000.061
boxplotSexGenotypeResult1.0500.0241.073
boxplotSexGenotypeWeightBatchAdjusted0.0560.0000.056
categoricalBarplot0.1090.0000.109
checkDataset0.0310.0000.031
classificationTag0.60.00.6
determiningLambda0.7260.0590.786
dim0.0320.0040.036
finalLRModel0.4650.0200.486
finalModel0.4890.0040.494
finalTFModel0.3750.0160.392
htestPhenStat-class0.1040.0080.113
modelFormula000
modelFormulaLR000
parserOutputSummary0.5860.0080.594
parserOutputSummaryLR0.4400.0080.447
parserOutputTFSummary0.080.000.08
performReverseTransformation0.0000.0000.001
performTransformation0.0010.0000.000
plot.PhenList2.0180.0352.055
plot.PhenTestResult2.0540.0612.114
plotResidualPredicted0.6140.0000.615
printLROutput0.4170.0040.421
printTabStyle0.0010.0000.001
qqplotGenotype0.6250.0070.634
qqplotRandomEffects0.6300.0030.635
qqplotRotatedResiduals3.7400.0483.787
recommendMethod0.170.000.17
scatterplotGenotypeWeight0.1440.0040.147
scatterplotGenotypeWeightResult0.8110.0350.848
scatterplotSexGenotypeBatch0.0820.0090.090
scatterplotSexGenotypeBatchResult0.7630.0110.775
startLRModel0.3690.0010.369
startModel0.4450.0000.445
startTFModel0.3220.0000.321
summaryOutput0.7290.0000.728
summaryPhenListResult0.7070.0040.712
testDataset2.0270.0162.044
testFinalLRModel0.4170.0000.417
testFinalModel0.7330.0000.732
vectorOutput0.6920.0020.694
vectorOutputMatrices0.1180.0010.120