Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-14 11:41 -0400 (Fri, 14 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
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 2174/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.15.0 (landing page) Michelle Webb
| 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 24.03 LTS) / aarch64 | 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: 1.15.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings tLOH_1.15.0.tar.gz |
StartedAt: 2025-03-14 02:56:37 -0400 (Fri, 14 Mar 2025) |
EndedAt: 2025-03-14 03:07:25 -0400 (Fri, 14 Mar 2025) |
EllapsedTime: 648.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings tLOH_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/tLOH.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘tLOH/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tLOH’ version ‘1.15.0’ * 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 loading without being on the library search path ... 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 71.567 2.116 77.697 regionAnalysis 52.370 0.550 55.155 runHMM_3 42.125 0.219 42.346 runHMM_2 41.757 0.234 41.992 prepareHMMdataframes 27.423 0.489 28.357 runHMM_1 24.782 0.194 24.985 tLOHCalcUpdate 24.075 0.098 24.180 splitByChromosome 23.639 0.028 23.666 alleleFrequencyPlot 6.773 0.289 7.063 aggregateCHRPlot 6.472 0.222 6.689 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/tLOH.Rcheck/00check.log’ for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘tLOH’ ... ** this is package ‘tLOH’ version ‘1.15.0’ ** 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 | 6.472 | 0.222 | 6.689 | |
alleleFrequencyPlot | 6.773 | 0.289 | 7.063 | |
documentErrorRegions | 0.002 | 0.000 | 0.002 | |
hiddenMarkovAnalysis | 71.567 | 2.116 | 77.697 | |
humanGBMsampleAC | 0.063 | 0.005 | 0.102 | |
initialStartProbabilities | 0.000 | 0.001 | 0.002 | |
marginalLikelihoodM1 | 0.005 | 0.000 | 0.005 | |
marginalLikelihoodM2 | 0.001 | 0.002 | 0.003 | |
marginalM1Calc | 0 | 0 | 0 | |
marginalM2CalcBHET | 0.002 | 0.000 | 0.002 | |
marginalM2CalcBLOH | 0.002 | 0.000 | 0.002 | |
modePeakCalc | 0.000 | 0.001 | 0.002 | |
prepareHMMdataframes | 27.423 | 0.489 | 28.357 | |
regionAnalysis | 52.370 | 0.550 | 55.155 | |
regionFinalize | 0 | 0 | 0 | |
removeOutlierFromCalc | 0.001 | 0.000 | 0.000 | |
runHMM_1 | 24.782 | 0.194 | 24.985 | |
runHMM_2 | 41.757 | 0.234 | 41.992 | |
runHMM_3 | 42.125 | 0.219 | 42.346 | |
splitByChromosome | 23.639 | 0.028 | 23.666 | |
summarizeRegions1 | 0.001 | 0.000 | 0.000 | |
summarizeRegions2 | 0.001 | 0.000 | 0.000 | |
tLOHCalc | 4.177 | 0.016 | 4.193 | |
tLOHCalcUpdate | 24.075 | 0.098 | 24.180 | |
tLOHDataImport | 0 | 0 | 0 | |