Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:57 -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 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 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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PhenStat_2.33.0.tar.gz
StartedAt: 2022-06-24 04:24:12 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:26:32 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 140.2 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 --force-multiarch --install=check:PhenStat.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings PhenStat_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/PhenStat.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 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 '2.33.0'
* 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 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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/PhenStat_2.33.0.tar.gz && rm -rf PhenStat.buildbin-libdir && mkdir PhenStat.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhenStat.buildbin-libdir PhenStat_2.33.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL PhenStat_2.33.0.zip && rm PhenStat_2.33.0.tar.gz PhenStat_2.33.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  734k  100  734k    0     0  6688k      0 --:--:-- --:--:-- --:--:-- 6736k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'PhenStat' as PhenStat_2.33.0.zip
* DONE (PhenStat)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'PhenStat' successfully unpacked and MD5 sums checked

Tests output

PhenStat.Rcheck/tests/runTests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
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 -- Fri Jun 24 04:26:19 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 
   3.23    0.31    3.50 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.140.010.16
JSONOutput0.920.070.99
LRDataset0.030.010.05
PhenList-class0.160.020.17
PhenList0.180.000.19
PhenStatReport0.050.000.04
PhenTestResult-class0.750.010.77
PhenTestResult0.780.020.80
RRTest0.130.030.15
TFDataset0.200.000.21
analysedDataset0.730.030.76
analysisResults0.750.020.78
boxplotResidualBatch0.770.030.80
boxplotSexGenotype0.080.000.08
boxplotSexGenotypeBatch0.120.000.12
boxplotSexGenotypeBatchAdjusted0.10.00.1
boxplotSexGenotypeResult1.250.011.26
boxplotSexGenotypeWeightBatchAdjusted0.070.000.08
categoricalBarplot0.100.050.14
checkDataset0.030.000.03
classificationTag0.750.000.75
determiningLambda1.090.311.41
dim0.050.000.05
finalLRModel0.590.000.59
finalModel0.690.000.69
finalTFModel0.440.000.44
htestPhenStat-class0.110.020.13
modelFormula000
modelFormulaLR000
parserOutputSummary0.750.010.76
parserOutputSummaryLR0.590.040.63
parserOutputTFSummary0.100.000.09
performReverseTransformation000
performTransformation000
plot.PhenList2.670.072.80
plot.PhenTestResult2.340.052.39
plotResidualPredicted0.910.000.90
printLROutput0.550.000.55
printTabStyle000
qqplotGenotype0.860.000.86
qqplotRandomEffects0.810.000.81
qqplotRotatedResiduals3.720.023.73
recommendMethod0.160.000.16
scatterplotGenotypeWeight0.120.010.14
scatterplotGenotypeWeightResult0.920.050.97
scatterplotSexGenotypeBatch0.080.000.08
scatterplotSexGenotypeBatchResult1.000.011.01
startLRModel0.890.020.91
startModel0.810.030.84
startTFModel0.360.030.39
summaryOutput0.930.050.97
summaryPhenListResult0.890.000.89
testDataset2.540.012.58
testFinalLRModel0.550.000.54
testFinalModel0.940.050.99
vectorOutput0.870.000.87
vectorOutputMatrices0.360.010.38