Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:39:41 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 |
Package 1527/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhenStat 2.39.0 (landing page) Hamed Haselimashhadi
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the PhenStat package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PhenStat |
Version: 2.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.39.0.tar.gz |
StartedAt: 2024-03-02 08:26:13 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 08:31:19 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 306.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhenStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PhenStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhenStat’ version ‘2.39.0’ * 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 whether startup messages can be suppressed ... 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 ... NOTE Documented arguments not in \usage in Rd file 'printLROutput.Rd': ‘effectValues’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'plot.PhenList.Rd': ‘\dots’ Argument items with no description in Rd file 'plot.PhenTestResult.Rd': ‘\dots’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed qqplotRotatedResiduals 7.069 0.122 8.940 plot.PhenList 4.313 0.116 5.452 plot.PhenTestResult 4.246 0.113 5.370 testDataset 4.184 0.122 5.284 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 -- Sat Mar 2 08:30:56 2024 *********************************************** 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 6.511 0.623 8.737
PhenStat.Rcheck/PhenStat-Ex.timings
name | user | system | elapsed | |
FisherExactTest | 0.348 | 0.037 | 0.511 | |
JSONOutput | 1.632 | 0.037 | 2.161 | |
LRDataset | 0.164 | 0.005 | 0.221 | |
PhenList-class | 0.322 | 0.019 | 0.437 | |
PhenList | 0.331 | 0.011 | 0.428 | |
PhenStatReport | 0.084 | 0.003 | 0.106 | |
PhenTestResult-class | 1.401 | 0.024 | 1.909 | |
PhenTestResult | 1.145 | 0.020 | 1.518 | |
RRTest | 0.188 | 0.007 | 0.270 | |
TFDataset | 0.624 | 0.011 | 0.817 | |
analysedDataset | 1.345 | 0.023 | 1.716 | |
analysisResults | 1.314 | 0.019 | 1.680 | |
boxplotResidualBatch | 1.393 | 0.015 | 1.758 | |
boxplotSexGenotype | 0.149 | 0.009 | 0.190 | |
boxplotSexGenotypeBatch | 0.289 | 0.009 | 0.372 | |
boxplotSexGenotypeBatchAdjusted | 0.132 | 0.004 | 0.285 | |
boxplotSexGenotypeResult | 1.690 | 0.022 | 2.140 | |
boxplotSexGenotypeWeightBatchAdjusted | 0.132 | 0.003 | 0.177 | |
categoricalBarplot | 0.564 | 0.012 | 0.739 | |
checkDataset | 0.072 | 0.002 | 0.093 | |
classificationTag | 1.288 | 0.014 | 1.679 | |
determiningLambda | 1.248 | 0.179 | 1.868 | |
dim | 0.070 | 0.002 | 0.087 | |
finalLRModel | 0.939 | 0.013 | 1.245 | |
finalModel | 1.116 | 0.012 | 1.455 | |
finalTFModel | 1.114 | 0.022 | 1.477 | |
htestPhenStat-class | 0.276 | 0.012 | 0.368 | |
modelFormula | 0.001 | 0.001 | 0.001 | |
modelFormulaLR | 0 | 0 | 0 | |
parserOutputSummary | 1.296 | 0.015 | 1.614 | |
parserOutputSummaryLR | 0.838 | 0.015 | 0.981 | |
parserOutputTFSummary | 0.236 | 0.005 | 0.278 | |
performReverseTransformation | 0 | 0 | 0 | |
performTransformation | 0.001 | 0.000 | 0.001 | |
plot.PhenList | 4.313 | 0.116 | 5.452 | |
plot.PhenTestResult | 4.246 | 0.113 | 5.370 | |
plotResidualPredicted | 1.354 | 0.027 | 1.695 | |
printLROutput | 0.857 | 0.015 | 1.141 | |
printTabStyle | 0.002 | 0.001 | 0.003 | |
qqplotGenotype | 1.352 | 0.021 | 1.705 | |
qqplotRandomEffects | 1.322 | 0.020 | 1.720 | |
qqplotRotatedResiduals | 7.069 | 0.122 | 8.940 | |
recommendMethod | 0.849 | 0.016 | 1.066 | |
scatterplotGenotypeWeight | 0.269 | 0.011 | 0.341 | |
scatterplotGenotypeWeightResult | 1.719 | 0.035 | 2.106 | |
scatterplotSexGenotypeBatch | 0.170 | 0.009 | 0.202 | |
scatterplotSexGenotypeBatchResult | 1.706 | 0.032 | 2.200 | |
startLRModel | 0.814 | 0.021 | 1.076 | |
startModel | 1.061 | 0.018 | 1.267 | |
startTFModel | 1.039 | 0.016 | 1.280 | |
summaryOutput | 1.596 | 0.030 | 2.035 | |
summaryPhenListResult | 1.583 | 0.028 | 1.924 | |
testDataset | 4.184 | 0.122 | 5.284 | |
testFinalLRModel | 0.848 | 0.014 | 1.104 | |
testFinalModel | 1.573 | 0.019 | 2.001 | |
vectorOutput | 1.589 | 0.033 | 2.007 | |
vectorOutputMatrices | 0.283 | 0.010 | 0.349 | |