Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:20 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 2142/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.10.0 (landing page) Michelle Webb
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | NA | ||||||||
To the developers/maintainers of the tLOH package: - 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: 1.10.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.10.0.tar.gz |
StartedAt: 2024-04-18 06:24:28 -0400 (Thu, 18 Apr 2024) |
EndedAt: 2024-04-18 06:34:48 -0400 (Thu, 18 Apr 2024) |
EllapsedTime: 619.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tLOH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tLOH_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/tLOH.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘tLOH/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘tLOH’ version ‘1.10.0’ * 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 ... OK * 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 R 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 51.345 2.290 58.014 regionAnalysis 36.156 1.298 40.247 runHMM_3 34.246 1.516 38.960 runHMM_2 31.912 1.272 35.673 tLOHCalcUpdate 20.128 0.888 23.105 runHMM_1 19.934 0.721 22.317 splitByChromosome 19.564 0.791 21.791 prepareHMMdataframes 18.712 0.707 20.921 aggregateCHRPlot 5.402 0.262 6.003 alleleFrequencyPlot 5.377 0.247 6.134 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/tLOH.Rcheck/00check.log’ for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 | 5.402 | 0.262 | 6.003 | |
alleleFrequencyPlot | 5.377 | 0.247 | 6.134 | |
documentErrorRegions | 0.001 | 0.001 | 0.002 | |
hiddenMarkovAnalysis | 51.345 | 2.290 | 58.014 | |
humanGBMsampleAC | 0.045 | 0.002 | 0.049 | |
initialStartProbabilities | 0.000 | 0.000 | 0.001 | |
marginalLikelihoodM1 | 0.001 | 0.001 | 0.002 | |
marginalLikelihoodM2 | 0.001 | 0.000 | 0.001 | |
marginalM1Calc | 0 | 0 | 0 | |
marginalM2CalcBHET | 0 | 0 | 0 | |
marginalM2CalcBLOH | 0 | 0 | 0 | |
modePeakCalc | 0.001 | 0.000 | 0.001 | |
prepareHMMdataframes | 18.712 | 0.707 | 20.921 | |
regionAnalysis | 36.156 | 1.298 | 40.247 | |
regionFinalize | 0.000 | 0.000 | 0.001 | |
removeOutlierFromCalc | 0.000 | 0.001 | 0.001 | |
runHMM_1 | 19.934 | 0.721 | 22.317 | |
runHMM_2 | 31.912 | 1.272 | 35.673 | |
runHMM_3 | 34.246 | 1.516 | 38.960 | |
splitByChromosome | 19.564 | 0.791 | 21.791 | |
summarizeRegions1 | 0.000 | 0.001 | 0.000 | |
summarizeRegions2 | 0 | 0 | 0 | |
tLOHCalc | 3.075 | 0.167 | 3.955 | |
tLOHCalcUpdate | 20.128 | 0.888 | 23.105 | |
tLOHDataImport | 0 | 0 | 0 | |