Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:47 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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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 1466/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhenStat 2.35.0 (landing page) Hamed Haselimashhadi
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: PhenStat |
Version: 2.35.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PhenStat_2.35.0.tar.gz |
StartedAt: 2023-02-28 11:10:37 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 11:13:34 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 177.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhenStat.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings PhenStat_2.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/PhenStat.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘PhenStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhenStat’ version ‘2.35.0’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed qqplotRotatedResiduals 8.646 0.032 8.679 * 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 ... ‘PhenStat.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.17-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 -- Tue Feb 28 11:13:00 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 3.845 0.180 4.007
PhenStat.Rcheck/PhenStat-Ex.timings
name | user | system | elapsed | |
FisherExactTest | 0.169 | 0.032 | 0.202 | |
JSONOutput | 1.090 | 0.004 | 1.095 | |
LRDataset | 0.059 | 0.000 | 0.059 | |
PhenList-class | 0.220 | 0.000 | 0.221 | |
PhenList | 0.220 | 0.000 | 0.224 | |
PhenStatReport | 0.044 | 0.000 | 0.044 | |
PhenTestResult-class | 0.934 | 0.036 | 0.970 | |
PhenTestResult | 0.752 | 0.000 | 0.752 | |
RRTest | 0.105 | 0.000 | 0.104 | |
TFDataset | 0.336 | 0.004 | 0.341 | |
analysedDataset | 0.889 | 0.012 | 0.901 | |
analysisResults | 0.885 | 0.004 | 0.888 | |
boxplotResidualBatch | 0.968 | 0.008 | 0.975 | |
boxplotSexGenotype | 0.091 | 0.020 | 0.112 | |
boxplotSexGenotypeBatch | 0.160 | 0.012 | 0.171 | |
boxplotSexGenotypeBatchAdjusted | 0.082 | 0.000 | 0.082 | |
boxplotSexGenotypeResult | 1.094 | 0.012 | 1.105 | |
boxplotSexGenotypeWeightBatchAdjusted | 0.092 | 0.000 | 0.092 | |
categoricalBarplot | 0.439 | 0.008 | 0.446 | |
checkDataset | 0.044 | 0.000 | 0.043 | |
classificationTag | 0.872 | 0.004 | 0.876 | |
determiningLambda | 1.184 | 0.020 | 1.204 | |
dim | 0.044 | 0.000 | 0.043 | |
finalLRModel | 0.603 | 0.008 | 0.615 | |
finalModel | 0.752 | 0.012 | 0.765 | |
finalTFModel | 0.583 | 0.036 | 0.620 | |
htestPhenStat-class | 0.159 | 0.004 | 0.162 | |
modelFormula | 0.000 | 0.001 | 0.000 | |
modelFormulaLR | 0 | 0 | 0 | |
parserOutputSummary | 0.877 | 0.014 | 0.890 | |
parserOutputSummaryLR | 0.805 | 0.016 | 0.822 | |
parserOutputTFSummary | 0.120 | 0.000 | 0.121 | |
performReverseTransformation | 0.001 | 0.000 | 0.000 | |
performTransformation | 0.001 | 0.000 | 0.000 | |
plot.PhenList | 3.031 | 0.016 | 3.048 | |
plot.PhenTestResult | 3.021 | 0.028 | 3.049 | |
plotResidualPredicted | 0.890 | 0.008 | 0.898 | |
printLROutput | 0.549 | 0.000 | 0.550 | |
printTabStyle | 0.001 | 0.000 | 0.001 | |
qqplotGenotype | 0.911 | 0.000 | 0.911 | |
qqplotRandomEffects | 0.911 | 0.004 | 0.915 | |
qqplotRotatedResiduals | 8.646 | 0.032 | 8.679 | |
recommendMethod | 0.319 | 0.016 | 0.334 | |
scatterplotGenotypeWeight | 0.169 | 0.000 | 0.170 | |
scatterplotGenotypeWeightResult | 1.120 | 0.004 | 1.125 | |
scatterplotSexGenotypeBatch | 0.098 | 0.004 | 0.102 | |
scatterplotSexGenotypeBatchResult | 1.100 | 0.004 | 1.104 | |
startLRModel | 0.510 | 0.004 | 0.514 | |
startModel | 0.540 | 0.016 | 0.556 | |
startTFModel | 0.535 | 0.012 | 0.547 | |
summaryOutput | 1.028 | 0.004 | 1.033 | |
summaryPhenListResult | 1.052 | 0.000 | 1.051 | |
testDataset | 2.989 | 0.012 | 3.001 | |
testFinalLRModel | 0.539 | 0.000 | 0.539 | |
testFinalModel | 1.203 | 0.008 | 1.211 | |
vectorOutput | 1.066 | 0.016 | 1.082 | |
vectorOutputMatrices | 0.166 | 0.000 | 0.166 | |