Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2158/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.14.0 (landing page) Michelle Webb
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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: 1.14.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tLOH_1.14.0.tar.gz |
StartedAt: 2024-12-20 06:49:06 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:02:30 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 804.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings tLOH_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/tLOH.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'tLOH/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tLOH' version '1.14.0' * 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 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 96.84 5.83 105.27 regionAnalysis 63.21 1.69 64.89 runHMM_3 61.82 1.99 63.79 runHMM_2 60.89 1.86 62.72 prepareHMMdataframes 40.17 1.05 41.98 runHMM_1 38.07 0.73 38.80 tLOHCalcUpdate 34.71 0.75 35.46 splitByChromosome 33.59 0.66 34.25 aggregateCHRPlot 9.23 0.19 9.42 alleleFrequencyPlot 8.34 0.17 8.52 tLOHCalc 5.95 0.11 6.06 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/tLOH.Rcheck/00check.log' for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 | 9.23 | 0.19 | 9.42 | |
alleleFrequencyPlot | 8.34 | 0.17 | 8.52 | |
documentErrorRegions | 0 | 0 | 0 | |
hiddenMarkovAnalysis | 96.84 | 5.83 | 105.27 | |
humanGBMsampleAC | 0.04 | 0.01 | 0.05 | |
initialStartProbabilities | 0 | 0 | 0 | |
marginalLikelihoodM1 | 0 | 0 | 0 | |
marginalLikelihoodM2 | 0 | 0 | 0 | |
marginalM1Calc | 0 | 0 | 0 | |
marginalM2CalcBHET | 0 | 0 | 0 | |
marginalM2CalcBLOH | 0.00 | 0.00 | 0.02 | |
modePeakCalc | 0 | 0 | 0 | |
prepareHMMdataframes | 40.17 | 1.05 | 41.98 | |
regionAnalysis | 63.21 | 1.69 | 64.89 | |
regionFinalize | 0 | 0 | 0 | |
removeOutlierFromCalc | 0 | 0 | 0 | |
runHMM_1 | 38.07 | 0.73 | 38.80 | |
runHMM_2 | 60.89 | 1.86 | 62.72 | |
runHMM_3 | 61.82 | 1.99 | 63.79 | |
splitByChromosome | 33.59 | 0.66 | 34.25 | |
summarizeRegions1 | 0 | 0 | 0 | |
summarizeRegions2 | 0 | 0 | 0 | |
tLOHCalc | 5.95 | 0.11 | 6.06 | |
tLOHCalcUpdate | 34.71 | 0.75 | 35.46 | |
tLOHDataImport | 0 | 0 | 0 | |