Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:59 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 2171/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.12.0 (landing page) Michelle Webb
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the tLOH package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tLOH.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: tLOH |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.12.0.tar.gz |
StartedAt: 2024-05-30 00:18:02 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 00:30:13 -0400 (Thu, 30 May 2024) |
EllapsedTime: 730.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘tLOH/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tLOH’ version ‘1.12.0’ * package encoding: UTF-8 * 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 ‘tLOH’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... NOTE Problems with news in ‘NEWS.md’: No news entries found. * 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 dependencies in R code ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed hiddenMarkovAnalysis 79.569 2.740 99.483 regionAnalysis 56.486 1.294 58.280 runHMM_2 49.268 1.267 51.089 runHMM_3 48.951 1.308 50.905 prepareHMMdataframes 29.547 0.737 35.544 runHMM_1 29.264 0.691 30.235 splitByChromosome 27.451 0.723 28.512 tLOHCalcUpdate 27.230 0.626 28.154 aggregateCHRPlot 7.919 0.338 8.340 alleleFrequencyPlot 7.880 0.215 8.181 tLOHCalc 4.955 0.095 5.094 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/tLOH.Rcheck/00check.log’ for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘tLOH’ ... ** using staged installation ** R ** data ** 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 (tLOH)
tLOH.Rcheck/tLOH-Ex.timings
name | user | system | elapsed | |
aggregateCHRPlot | 7.919 | 0.338 | 8.340 | |
alleleFrequencyPlot | 7.880 | 0.215 | 8.181 | |
documentErrorRegions | 0.002 | 0.001 | 0.005 | |
hiddenMarkovAnalysis | 79.569 | 2.740 | 99.483 | |
humanGBMsampleAC | 0.051 | 0.003 | 0.102 | |
initialStartProbabilities | 0.001 | 0.002 | 0.004 | |
marginalLikelihoodM1 | 0.004 | 0.001 | 0.005 | |
marginalLikelihoodM2 | 0.003 | 0.001 | 0.003 | |
marginalM1Calc | 0.001 | 0.001 | 0.001 | |
marginalM2CalcBHET | 0.002 | 0.001 | 0.002 | |
marginalM2CalcBLOH | 0.002 | 0.001 | 0.002 | |
modePeakCalc | 0.002 | 0.000 | 0.003 | |
prepareHMMdataframes | 29.547 | 0.737 | 35.544 | |
regionAnalysis | 56.486 | 1.294 | 58.280 | |
regionFinalize | 0.000 | 0.000 | 0.001 | |
removeOutlierFromCalc | 0 | 0 | 0 | |
runHMM_1 | 29.264 | 0.691 | 30.235 | |
runHMM_2 | 49.268 | 1.267 | 51.089 | |
runHMM_3 | 48.951 | 1.308 | 50.905 | |
splitByChromosome | 27.451 | 0.723 | 28.512 | |
summarizeRegions1 | 0.001 | 0.000 | 0.000 | |
summarizeRegions2 | 0.000 | 0.000 | 0.001 | |
tLOHCalc | 4.955 | 0.095 | 5.094 | |
tLOHCalcUpdate | 27.230 | 0.626 | 28.154 | |
tLOHDataImport | 0 | 0 | 0 | |