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This page was generated on 2021-07-21 15:05:05 -0400 (Wed, 21 Jul 2021).

CHECK results for PhenStat on nebbiolo1

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: 2021-07-20 04:50:13 -0400 (Tue, 20 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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PhenStat_2.28.0.tar.gz
StartedAt: 2021-07-20 11:01:18 -0400 (Tue, 20 Jul 2021)
EndedAt: 2021-07-20 11:03:11 -0400 (Tue, 20 Jul 2021)
EllapsedTime: 112.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings PhenStat_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/PhenStat.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘2.28.0’
* 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 ... 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-3.13-bioc/meat/PhenStat.Rcheck/00check.log’
for details.



Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 -- Tue Jul 20 11:03:06 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 
  3.000   0.160   3.145 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.1400.0120.153
JSONOutput0.7790.0080.788
LRDataset0.0530.0000.055
PhenList-class0.2040.0080.215
PhenList0.1530.0040.157
PhenStatReport0.0330.0000.033
PhenTestResult-class0.6910.0120.704
PhenTestResult0.5880.0080.597
RRTest0.0750.0000.075
TFDataset0.2160.0080.224
analysedDataset0.6260.0080.635
analysisResults0.6490.0000.649
boxplotResidualBatch0.9340.0080.942
boxplotSexGenotype0.060.000.06
boxplotSexGenotypeBatch0.1130.0040.117
boxplotSexGenotypeBatchAdjusted0.0550.0000.056
boxplotSexGenotypeResult0.7720.0160.788
boxplotSexGenotypeWeightBatchAdjusted0.0570.0000.057
categoricalBarplot0.1110.0040.115
checkDataset0.0320.0000.032
classificationTag0.6180.0040.622
determiningLambda0.6280.0080.637
dim0.0360.0040.040
finalLRModel0.3690.0120.381
finalModel0.5040.0040.508
finalTFModel0.3830.0120.396
htestPhenStat-class0.1150.0040.118
modelFormula0.0010.0000.000
modelFormulaLR0.0010.0000.000
parserOutputSummary0.6440.0040.648
parserOutputSummaryLR0.3840.0080.393
parserOutputTFSummary0.0810.0000.082
performReverseTransformation0.0010.0000.001
performTransformation000
plot.PhenList2.0190.0242.043
plot.PhenTestResult2.2400.0442.284
plotResidualPredicted0.5950.0080.602
printLROutput0.3650.0000.364
printTabStyle0.0000.0010.001
qqplotGenotype0.6270.0110.638
qqplotRandomEffects0.6470.0040.649
qqplotRotatedResiduals3.5150.0523.568
recommendMethod0.1790.0000.178
scatterplotGenotypeWeight0.1430.0000.144
scatterplotGenotypeWeightResult0.8350.0120.846
scatterplotSexGenotypeBatch0.0830.0000.084
scatterplotSexGenotypeBatchResult0.7890.0040.793
startLRModel0.3220.0040.325
startModel0.4680.0040.471
startTFModel0.3440.0040.348
summaryOutput0.7400.0160.755
summaryPhenListResult0.7170.0160.733
testDataset2.0230.0202.043
testFinalLRModel0.3370.0080.345
testFinalModel0.7790.0200.799
vectorOutput0.7300.0190.750
vectorOutputMatrices0.1040.0000.104