Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:45 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (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 |
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. |
Package 1475/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhenStat 2.34.0 (landing page) Hamed Haselimashhadi
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
PhenStat.Rcheck/PhenStat-Ex.timings
name | user | system | elapsed | |
FisherExactTest | 0.15 | 0.00 | 0.17 | |
JSONOutput | 0.94 | 0.02 | 0.95 | |
LRDataset | 0.06 | 0.00 | 0.07 | |
PhenList-class | 0.25 | 0.01 | 0.26 | |
PhenList | 0.19 | 0.04 | 0.22 | |
PhenStatReport | 0.03 | 0.00 | 0.03 | |
PhenTestResult-class | 0.75 | 0.01 | 0.77 | |
PhenTestResult | 0.67 | 0.00 | 0.67 | |
RRTest | 0.08 | 0.00 | 0.08 | |
TFDataset | 0.16 | 0.02 | 0.17 | |
analysedDataset | 0.72 | 0.04 | 0.77 | |
analysisResults | 0.73 | 0.02 | 0.75 | |
boxplotResidualBatch | 1.06 | 0.03 | 1.09 | |
boxplotSexGenotype | 0.10 | 0.00 | 0.09 | |
boxplotSexGenotypeBatch | 0.15 | 0.00 | 0.16 | |
boxplotSexGenotypeBatchAdjusted | 0.07 | 0.00 | 0.06 | |
boxplotSexGenotypeResult | 0.98 | 0.00 | 0.99 | |
boxplotSexGenotypeWeightBatchAdjusted | 0.06 | 0.00 | 0.06 | |
categoricalBarplot | 0.11 | 0.00 | 0.11 | |
checkDataset | 0.05 | 0.00 | 0.05 | |
classificationTag | 0.78 | 0.00 | 0.78 | |
determiningLambda | 1.02 | 0.37 | 1.39 | |
dim | 0.03 | 0.00 | 0.03 | |
finalLRModel | 0.53 | 0.02 | 0.57 | |
finalModel | 0.66 | 0.00 | 0.65 | |
finalTFModel | 0.36 | 0.00 | 0.36 | |
htestPhenStat-class | 0.10 | 0.00 | 0.11 | |
modelFormula | 0 | 0 | 0 | |
modelFormulaLR | 0 | 0 | 0 | |
parserOutputSummary | 0.88 | 0.00 | 0.88 | |
parserOutputSummaryLR | 0.56 | 0.00 | 0.56 | |
parserOutputTFSummary | 0.08 | 0.00 | 0.08 | |
performReverseTransformation | 0 | 0 | 0 | |
performTransformation | 0 | 0 | 0 | |
plot.PhenList | 3.28 | 0.12 | 3.41 | |
plot.PhenTestResult | 2.28 | 0.06 | 2.34 | |
plotResidualPredicted | 0.73 | 0.00 | 0.74 | |
printLROutput | 0.5 | 0.0 | 0.5 | |
printTabStyle | 0 | 0 | 0 | |
qqplotGenotype | 0.78 | 0.00 | 0.78 | |
qqplotRandomEffects | 1.05 | 0.00 | 1.05 | |
qqplotRotatedResiduals | 3.31 | 0.04 | 3.34 | |
recommendMethod | 0.16 | 0.01 | 0.17 | |
scatterplotGenotypeWeight | 0.12 | 0.00 | 0.13 | |
scatterplotGenotypeWeightResult | 0.97 | 0.00 | 0.97 | |
scatterplotSexGenotypeBatch | 0.08 | 0.00 | 0.08 | |
scatterplotSexGenotypeBatchResult | 0.93 | 0.00 | 0.94 | |
startLRModel | 0.52 | 0.02 | 0.53 | |
startModel | 0.67 | 0.00 | 0.67 | |
startTFModel | 0.33 | 0.00 | 0.33 | |
summaryOutput | 0.83 | 0.01 | 0.84 | |
summaryPhenListResult | 0.83 | 0.03 | 0.86 | |
testDataset | 2.56 | 0.03 | 2.61 | |
testFinalLRModel | 0.51 | 0.00 | 0.52 | |
testFinalModel | 0.86 | 0.02 | 0.87 | |
vectorOutput | 0.83 | 0.03 | 0.86 | |
vectorOutputMatrices | 0.13 | 0.00 | 0.12 | |