Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:48 -0400 (Fri, 15 Oct 2021).
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. |
Package 1383/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhenStat 2.28.0 (landing page) Hamed Haselimashhadi
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
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: 2021-10-14 11:00:55 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:02:50 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 114.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhenStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 4.1.1 (2021-08-10) * 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.
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)
PhenStat.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" 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 -- Thu Oct 14 11:02:46 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 3.446 0.304 3.736
PhenStat.Rcheck/PhenStat-Ex.timings
name | user | system | elapsed | |
FisherExactTest | 0.145 | 0.008 | 0.155 | |
JSONOutput | 0.761 | 0.008 | 0.770 | |
LRDataset | 0.052 | 0.001 | 0.054 | |
PhenList-class | 0.208 | 0.011 | 0.223 | |
PhenList | 0.161 | 0.000 | 0.161 | |
PhenStatReport | 0.032 | 0.000 | 0.032 | |
PhenTestResult-class | 0.640 | 0.008 | 0.647 | |
PhenTestResult | 0.517 | 0.008 | 0.525 | |
RRTest | 0.065 | 0.004 | 0.069 | |
TFDataset | 0.198 | 0.000 | 0.198 | |
analysedDataset | 0.596 | 0.015 | 0.612 | |
analysisResults | 0.608 | 0.000 | 0.609 | |
boxplotResidualBatch | 0.697 | 0.012 | 0.710 | |
boxplotSexGenotype | 0.074 | 0.000 | 0.075 | |
boxplotSexGenotypeBatch | 0.112 | 0.000 | 0.112 | |
boxplotSexGenotypeBatchAdjusted | 0.059 | 0.000 | 0.059 | |
boxplotSexGenotypeResult | 0.791 | 0.008 | 0.799 | |
boxplotSexGenotypeWeightBatchAdjusted | 0.059 | 0.004 | 0.062 | |
categoricalBarplot | 0.132 | 0.008 | 0.141 | |
checkDataset | 0.037 | 0.000 | 0.036 | |
classificationTag | 0.647 | 0.008 | 0.655 | |
determiningLambda | 1.208 | 0.360 | 1.567 | |
dim | 0.036 | 0.000 | 0.037 | |
finalLRModel | 0.418 | 0.012 | 0.430 | |
finalModel | 0.492 | 0.024 | 0.516 | |
finalTFModel | 0.366 | 0.080 | 0.446 | |
htestPhenStat-class | 0.089 | 0.024 | 0.114 | |
modelFormula | 0.001 | 0.000 | 0.001 | |
modelFormulaLR | 0.000 | 0.000 | 0.001 | |
parserOutputSummary | 0.624 | 0.000 | 0.623 | |
parserOutputSummaryLR | 0.364 | 0.009 | 0.374 | |
parserOutputTFSummary | 0.088 | 0.002 | 0.090 | |
performReverseTransformation | 0.000 | 0.001 | 0.000 | |
performTransformation | 0 | 0 | 0 | |
plot.PhenList | 2.011 | 0.006 | 2.017 | |
plot.PhenTestResult | 1.999 | 0.028 | 2.027 | |
plotResidualPredicted | 0.645 | 0.000 | 0.645 | |
printLROutput | 0.355 | 0.004 | 0.360 | |
printTabStyle | 0.001 | 0.000 | 0.001 | |
qqplotGenotype | 0.680 | 0.004 | 0.684 | |
qqplotRandomEffects | 0.638 | 0.003 | 0.642 | |
qqplotRotatedResiduals | 3.491 | 0.036 | 3.527 | |
recommendMethod | 0.185 | 0.000 | 0.184 | |
scatterplotGenotypeWeight | 0.142 | 0.000 | 0.143 | |
scatterplotGenotypeWeightResult | 0.837 | 0.004 | 0.841 | |
scatterplotSexGenotypeBatch | 0.074 | 0.004 | 0.077 | |
scatterplotSexGenotypeBatchResult | 0.801 | 0.000 | 0.801 | |
startLRModel | 0.307 | 0.004 | 0.311 | |
startModel | 0.48 | 0.00 | 0.48 | |
startTFModel | 0.339 | 0.004 | 0.343 | |
summaryOutput | 0.726 | 0.004 | 0.731 | |
summaryPhenListResult | 0.725 | 0.000 | 0.726 | |
testDataset | 2.185 | 0.008 | 2.193 | |
testFinalLRModel | 0.355 | 0.004 | 0.359 | |
testFinalModel | 0.8 | 0.0 | 0.8 | |
vectorOutput | 1.071 | 0.004 | 1.075 | |
vectorOutputMatrices | 0.101 | 0.002 | 0.103 | |