Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 517/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decompTumor2Sig 2.22.0 (landing page) Rosario M. Piro
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | TIMEOUT | skipped | skipped | |||||||||
To the developers/maintainers of the decompTumor2Sig package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decompTumor2Sig.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: decompTumor2Sig |
Version: 2.22.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.22.0.tar.gz |
StartedAt: 2024-12-20 00:42:08 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:49:55 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 467.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/decompTumor2Sig.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'decompTumor2Sig/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'decompTumor2Sig' version '2.22.0' * 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 'decompTumor2Sig' 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 ... NOTE File inst/LICENSE will install at top-level and is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * 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 whether startup messages can be suppressed ... 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotExplainedVariance 84.13 1.02 85.23 convertGenomesFromVRanges 7.89 0.76 9.78 decomposeTumorGenomes 4.04 0.55 5.05 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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-3.20-bioc/meat/decompTumor2Sig.Rcheck/00check.log' for details.
decompTumor2Sig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'decompTumor2Sig' ... ** using staged installation ** R ** 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 (decompTumor2Sig)
decompTumor2Sig.Rcheck/decompTumor2Sig-Ex.timings
name | user | system | elapsed | |
adjustSignaturesForRegionSet | 3.48 | 0.22 | 4.72 | |
composeGenomesFromExposures | 0.20 | 0.04 | 0.89 | |
computeExplainedVariance | 0.21 | 0.05 | 0.66 | |
convertAlexandrov2Shiraishi | 0.06 | 0.02 | 0.46 | |
convertGenomesFromVRanges | 7.89 | 0.76 | 9.78 | |
decomposeTumorGenomes | 4.04 | 0.55 | 5.05 | |
determineSignatureDistances | 0.10 | 0.00 | 0.48 | |
downgradeShiraishiSignatures | 0.00 | 0.00 | 0.02 | |
evaluateDecompositionQuality | 0.23 | 0.00 | 0.62 | |
getGenomesFromMutFeatData | 0.30 | 0.00 | 0.32 | |
getSignaturesFromEstParam | 0.14 | 0.00 | 0.14 | |
isAlexandrovSet | 0.05 | 0.00 | 0.45 | |
isExposureSet | 3.43 | 0.65 | 4.50 | |
isShiraishiSet | 0.07 | 0.00 | 0.45 | |
isSignatureSet | 0.00 | 0.02 | 0.41 | |
mapSignatureSets | 0.09 | 0.00 | 0.49 | |
plotDecomposedContribution | 0.56 | 0.01 | 0.97 | |
plotExplainedVariance | 84.13 | 1.02 | 85.23 | |
plotMutationDistribution | 2.37 | 0.03 | 2.83 | |
readAlexandrovSignatures | 0.03 | 0.01 | 0.44 | |
readGenomesFromMPF | 3.22 | 0.58 | 3.81 | |
readGenomesFromVCF | 4.28 | 0.53 | 4.81 | |
readShiraishiSignatures | 0 | 0 | 0 | |
sameSignatureFormat | 0.09 | 0.00 | 0.47 | |