Back to Build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-07 15:40 -0400 (Sat, 07 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4711 |
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 | |||||||||
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: 2024-09-07 01:50:18 -0400 (Sat, 07 Sep 2024) |
EndedAt: 2024-09-07 02:00:32 -0400 (Sat, 07 Sep 2024) |
EllapsedTime: 614.2 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 22.04.4 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 60.098 0.772 60.858 regionAnalysis 45.719 0.260 45.979 runHMM_3 41.424 0.180 41.605 runHMM_2 41.250 0.132 41.383 runHMM_1 24.600 0.096 24.696 tLOHCalcUpdate 23.837 0.208 24.043 prepareHMMdataframes 23.447 0.096 23.543 splitByChromosome 23.477 0.040 23.517 alleleFrequencyPlot 6.697 0.200 6.897 aggregateCHRPlot 6.332 0.236 6.559 * 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 | 6.332 | 0.236 | 6.559 | |
alleleFrequencyPlot | 6.697 | 0.200 | 6.897 | |
documentErrorRegions | 0.002 | 0.000 | 0.001 | |
hiddenMarkovAnalysis | 60.098 | 0.772 | 60.858 | |
humanGBMsampleAC | 0.04 | 0.00 | 0.04 | |
initialStartProbabilities | 0.001 | 0.000 | 0.000 | |
marginalLikelihoodM1 | 0.002 | 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 | 23.447 | 0.096 | 23.543 | |
regionAnalysis | 45.719 | 0.260 | 45.979 | |
regionFinalize | 0 | 0 | 0 | |
removeOutlierFromCalc | 0.000 | 0.000 | 0.001 | |
runHMM_1 | 24.600 | 0.096 | 24.696 | |
runHMM_2 | 41.250 | 0.132 | 41.383 | |
runHMM_3 | 41.424 | 0.180 | 41.605 | |
splitByChromosome | 23.477 | 0.040 | 23.517 | |
summarizeRegions1 | 0 | 0 | 0 | |
summarizeRegions2 | 0 | 0 | 0 | |
tLOHCalc | 4.216 | 0.000 | 4.216 | |
tLOHCalcUpdate | 23.837 | 0.208 | 24.043 | |
tLOHDataImport | 0 | 0 | 0 | |