Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-12 11:41 -0400 (Thu, 12 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4713 |
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4450 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4483 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4430 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4428 |
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 2130/2258 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.13.0 (landing page) Michelle Webb
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.13.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tLOH_1.13.0.tar.gz |
StartedAt: 2024-09-12 03:57:23 -0400 (Thu, 12 Sep 2024) |
EndedAt: 2024-09-12 04:12:21 -0400 (Thu, 12 Sep 2024) |
EllapsedTime: 898.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:tLOH.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings tLOH_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/tLOH.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘tLOH/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tLOH’ version ‘1.13.0’ * 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 95.764 1.171 97.310 regionAnalysis 72.631 1.115 80.937 runHMM_3 68.407 0.305 68.953 runHMM_2 67.484 0.339 75.714 runHMM_1 42.026 0.504 51.403 splitByChromosome 39.309 0.631 40.077 tLOHCalcUpdate 37.701 0.184 37.933 prepareHMMdataframes 36.807 0.160 37.070 alleleFrequencyPlot 11.100 0.324 11.461 aggregateCHRPlot 9.651 0.344 10.009 tLOHCalc 7.473 0.008 7.527 * 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-3.20-bioc/meat/tLOH.Rcheck/00check.log’ for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 | 9.651 | 0.344 | 10.009 | |
alleleFrequencyPlot | 11.100 | 0.324 | 11.461 | |
documentErrorRegions | 0.003 | 0.000 | 0.003 | |
hiddenMarkovAnalysis | 95.764 | 1.171 | 97.310 | |
humanGBMsampleAC | 0.039 | 0.000 | 0.039 | |
initialStartProbabilities | 0.001 | 0.000 | 0.001 | |
marginalLikelihoodM1 | 0.003 | 0.000 | 0.002 | |
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 | 36.807 | 0.160 | 37.070 | |
regionAnalysis | 72.631 | 1.115 | 80.937 | |
regionFinalize | 0.000 | 0.000 | 0.001 | |
removeOutlierFromCalc | 0.001 | 0.000 | 0.001 | |
runHMM_1 | 42.026 | 0.504 | 51.403 | |
runHMM_2 | 67.484 | 0.339 | 75.714 | |
runHMM_3 | 68.407 | 0.305 | 68.953 | |
splitByChromosome | 39.309 | 0.631 | 40.077 | |
summarizeRegions1 | 0.001 | 0.000 | 0.001 | |
summarizeRegions2 | 0 | 0 | 0 | |
tLOHCalc | 7.473 | 0.008 | 7.527 | |
tLOHCalcUpdate | 37.701 | 0.184 | 37.933 | |
tLOHDataImport | 0.001 | 0.000 | 0.000 | |