Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1534/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhenStat 2.43.0 (landing page) Hamed Haselimashhadi
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | 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: 2.43.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhenStat_2.43.0.tar.gz |
StartedAt: 2024-12-24 00:54:54 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 00:56:55 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 120.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhenStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhenStat_2.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PhenStat.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘PhenStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhenStat’ version ‘2.43.0’ * 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 code 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 loading without being on the library search path ... 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 ... NOTE checkRd: (-1) plot.PhenList.Rd:49-53: Lost braces 49 | \item boxplotSexGenotype. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:54-58: Lost braces 54 | \item boxplotSexGenotypeBatchAdjusted. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:59-63: Lost braces 59 | \item boxplotSexGenotypeWeightBatchAdjusted. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:64-68: Lost braces 64 | \item scatterplotSexGenotypeBatch. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:69-73: Lost braces 69 | \item scatterplotGenotypeWeight. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:74-78: Lost braces 74 | \item boxplotSexGenotypeBatch. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:41-45: Lost braces 41 | \item boxplotSexGenotypeResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:46-50: Lost braces 46 | \item scatterplotSexGenotypeBatchResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:51-55: Lost braces 51 | \item scatterplotGenotypeWeightResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:56-60: Lost braces 56 | \item plotResidualPredicted. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:61-65: Lost braces 61 | \item qqplotRandomEffects. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:66-70: Lost braces 66 | \item boxplotResidualBatch. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:71-75: Lost braces 71 | \item qqplotRotatedResiduals. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:76-80: Lost braces 76 | \item qqplotGenotype. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:81-85: Lost braces 81 | \item categoricalBarplot. See documentations for { | ^ checkRd: (-1) qqplotRotatedResiduals.Rd:18: Lost braces 18 | Houseman, E. A., Ryan, L. M., Coull, B. A. (2004): Cholesky residuals for assessing normal errors in a linear model with correlated outcomes. \emph{Journal of the American Statistical Association} \bold{99}{466}: pg 383-394. Doi 10.1198 | ^ * 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 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 ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 Dec 24 00:56:39 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 2.446 0.203 2.638
PhenStat.Rcheck/PhenStat-Ex.timings
name | user | system | elapsed | |
FisherExactTest | 0.445 | 0.017 | 0.463 | |
JSONOutput | 0.727 | 0.022 | 0.750 | |
LRDataset | 0.040 | 0.000 | 0.041 | |
PhenList-class | 0.146 | 0.005 | 0.152 | |
PhenList | 0.156 | 0.000 | 0.156 | |
PhenStatReport | 0.031 | 0.000 | 0.032 | |
PhenTestResult-class | 0.616 | 0.008 | 0.625 | |
PhenTestResult | 0.518 | 0.005 | 0.523 | |
RRTest | 0.068 | 0.003 | 0.071 | |
TFDataset | 0.207 | 0.002 | 0.209 | |
analysedDataset | 0.584 | 0.018 | 0.603 | |
analysisResults | 0.588 | 0.001 | 0.590 | |
boxplotResidualBatch | 0.616 | 0.000 | 0.616 | |
boxplotSexGenotype | 0.069 | 0.002 | 0.072 | |
boxplotSexGenotypeBatch | 0.11 | 0.00 | 0.11 | |
boxplotSexGenotypeBatchAdjusted | 0.053 | 0.000 | 0.054 | |
boxplotSexGenotypeResult | 0.724 | 0.005 | 0.729 | |
boxplotSexGenotypeWeightBatchAdjusted | 0.062 | 0.002 | 0.065 | |
categoricalBarplot | 0.114 | 0.002 | 0.116 | |
checkDataset | 0.030 | 0.001 | 0.030 | |
classificationTag | 0.829 | 0.003 | 0.832 | |
determiningLambda | 0.794 | 0.019 | 0.813 | |
dim | 0.032 | 0.000 | 0.032 | |
finalLRModel | 0.427 | 0.003 | 0.430 | |
finalModel | 0.482 | 0.026 | 0.510 | |
finalTFModel | 0.403 | 0.021 | 0.426 | |
htestPhenStat-class | 0.102 | 0.009 | 0.111 | |
modelFormula | 0.000 | 0.000 | 0.001 | |
modelFormulaLR | 0.000 | 0.000 | 0.001 | |
parserOutputSummary | 0.581 | 0.005 | 0.587 | |
parserOutputSummaryLR | 0.366 | 0.003 | 0.368 | |
parserOutputTFSummary | 0.079 | 0.001 | 0.079 | |
performReverseTransformation | 0.001 | 0.000 | 0.001 | |
performTransformation | 0.001 | 0.000 | 0.000 | |
plot.PhenList | 1.986 | 0.043 | 2.029 | |
plot.PhenTestResult | 1.964 | 0.020 | 1.983 | |
plotResidualPredicted | 0.589 | 0.002 | 0.591 | |
printLROutput | 0.385 | 0.001 | 0.386 | |
printTabStyle | 0.000 | 0.000 | 0.001 | |
qqplotGenotype | 0.606 | 0.001 | 0.607 | |
qqplotRandomEffects | 0.596 | 0.003 | 0.599 | |
qqplotRotatedResiduals | 3.533 | 0.058 | 3.591 | |
recommendMethod | 0.176 | 0.000 | 0.177 | |
scatterplotGenotypeWeight | 0.125 | 0.003 | 0.127 | |
scatterplotGenotypeWeightResult | 0.751 | 0.001 | 0.751 | |
scatterplotSexGenotypeBatch | 0.069 | 0.003 | 0.074 | |
scatterplotSexGenotypeBatchResult | 0.748 | 0.003 | 0.751 | |
startLRModel | 0.355 | 0.002 | 0.356 | |
startModel | 0.439 | 0.003 | 0.441 | |
startTFModel | 0.343 | 0.005 | 0.349 | |
summaryOutput | 0.731 | 0.035 | 0.765 | |
summaryPhenListResult | 0.707 | 0.004 | 0.711 | |
testDataset | 2.137 | 0.058 | 2.196 | |
testFinalLRModel | 0.377 | 0.004 | 0.381 | |
testFinalModel | 0.749 | 0.005 | 0.755 | |
vectorOutput | 0.671 | 0.005 | 0.676 | |
vectorOutputMatrices | 0.100 | 0.003 | 0.103 | |