Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:54 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the tLOH package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2036/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
tLOH 1.7.0 (landing page) Michelle Webb
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
Package: tLOH |
Version: 1.7.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings tLOH_1.7.0.tar.gz |
StartedAt: 2022-12-29 04:13:19 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 04:22:53 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 573.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: tLOH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tLOH.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings tLOH_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/tLOH.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'tLOH/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tLOH' version '1.7.0' * 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 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 61.69 2.41 64.13 regionAnalysis 51.85 0.46 54.47 runHMM_2 45.05 0.47 45.52 runHMM_3 42.43 0.22 42.67 runHMM_1 37.92 0.17 38.42 prepareHMMdataframes 29.26 0.17 29.43 tLOHCalcUpdate 28.30 0.09 28.39 splitByChromosome 28.22 0.07 28.31 alleleFrequencyPlot 6.50 0.06 6.58 aggregateCHRPlot 6.18 0.18 6.34 * 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 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/tLOH.Rcheck/00check.log' for details.
tLOH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL tLOH ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 | 6.18 | 0.18 | 6.34 | |
alleleFrequencyPlot | 6.50 | 0.06 | 6.58 | |
documentErrorRegions | 0 | 0 | 0 | |
hiddenMarkovAnalysis | 61.69 | 2.41 | 64.13 | |
humanGBMsampleAC | 0.03 | 0.00 | 0.03 | |
initialStartProbabilities | 0.00 | 0.01 | 0.02 | |
marginalLikelihoodM1 | 0 | 0 | 0 | |
marginalLikelihoodM2 | 0 | 0 | 0 | |
marginalM1Calc | 0 | 0 | 0 | |
marginalM2CalcBHET | 0 | 0 | 0 | |
marginalM2CalcBLOH | 0 | 0 | 0 | |
modePeakCalc | 0 | 0 | 0 | |
prepareHMMdataframes | 29.26 | 0.17 | 29.43 | |
regionAnalysis | 51.85 | 0.46 | 54.47 | |
regionFinalize | 0 | 0 | 0 | |
removeOutlierFromCalc | 0 | 0 | 0 | |
runHMM_1 | 37.92 | 0.17 | 38.42 | |
runHMM_2 | 45.05 | 0.47 | 45.52 | |
runHMM_3 | 42.43 | 0.22 | 42.67 | |
splitByChromosome | 28.22 | 0.07 | 28.31 | |
summarizeRegions1 | 0 | 0 | 0 | |
summarizeRegions2 | 0.00 | 0.02 | 0.02 | |
tLOHCalc | 4.53 | 0.00 | 4.53 | |
tLOHCalcUpdate | 28.30 | 0.09 | 28.39 | |
tLOHDataImport | 0 | 0 | 0 | |