Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 2199/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.17.0 (landing page) Michelle Webb
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | 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: 1.17.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings tLOH_1.17.0.tar.gz |
StartedAt: 2025-09-20 05:14:42 -0400 (Sat, 20 Sep 2025) |
EndedAt: 2025-09-20 05:26:07 -0400 (Sat, 20 Sep 2025) |
EllapsedTime: 684.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings tLOH_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/tLOH.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * 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 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘tLOH/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tLOH’ version ‘1.17.0’ * 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 72.454 0.823 74.997 regionAnalysis 52.480 0.301 55.837 runHMM_2 43.200 0.339 43.541 runHMM_3 42.482 0.152 42.635 prepareHMMdataframes 32.532 0.323 36.686 runHMM_1 25.947 0.039 25.987 tLOHCalcUpdate 24.030 0.045 24.076 splitByChromosome 23.916 0.115 24.031 aggregateCHRPlot 8.284 0.207 6.525 alleleFrequencyPlot 6.999 0.199 7.199 * 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-3.22-bioc/meat/tLOH.Rcheck/00check.log’ for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘tLOH’ ... ** this is package ‘tLOH’ version ‘1.17.0’ ** 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 | 8.284 | 0.207 | 6.525 | |
alleleFrequencyPlot | 6.999 | 0.199 | 7.199 | |
documentErrorRegions | 0.002 | 0.000 | 0.001 | |
hiddenMarkovAnalysis | 72.454 | 0.823 | 74.997 | |
humanGBMsampleAC | 0.044 | 0.001 | 0.044 | |
initialStartProbabilities | 0.001 | 0.000 | 0.001 | |
marginalLikelihoodM1 | 0.003 | 0.000 | 0.003 | |
marginalLikelihoodM2 | 0.001 | 0.000 | 0.001 | |
marginalM1Calc | 0 | 0 | 0 | |
marginalM2CalcBHET | 0.001 | 0.000 | 0.001 | |
marginalM2CalcBLOH | 0.001 | 0.000 | 0.001 | |
modePeakCalc | 0.001 | 0.000 | 0.001 | |
prepareHMMdataframes | 32.532 | 0.323 | 36.686 | |
regionAnalysis | 52.480 | 0.301 | 55.837 | |
regionFinalize | 0 | 0 | 0 | |
removeOutlierFromCalc | 0.000 | 0.000 | 0.001 | |
runHMM_1 | 25.947 | 0.039 | 25.987 | |
runHMM_2 | 43.200 | 0.339 | 43.541 | |
runHMM_3 | 42.482 | 0.152 | 42.635 | |
splitByChromosome | 23.916 | 0.115 | 24.031 | |
summarizeRegions1 | 0 | 0 | 0 | |
summarizeRegions2 | 0.000 | 0.000 | 0.001 | |
tLOHCalc | 4.332 | 0.012 | 4.344 | |
tLOHCalcUpdate | 24.030 | 0.045 | 24.076 | |
tLOHDataImport | 0 | 0 | 0 | |