Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4816 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4605 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4549 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 528/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decompTumor2Sig 2.25.1 (landing page) Rosario M. Piro
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | TIMEOUT | skipped | skipped | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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: 2.25.1 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decompTumor2Sig_2.25.1.tar.gz |
StartedAt: 2025-09-22 20:27:50 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 20:35:24 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 454.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decompTumor2Sig_2.25.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/decompTumor2Sig.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decompTumor2Sig’ version ‘2.25.1’ * 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 ‘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 78.408 0.467 79.409 convertGenomesFromVRanges 7.300 0.623 8.069 readGenomesFromVCF 5.420 0.530 6.470 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/decompTumor2Sig.Rcheck/00check.log’ for details.
decompTumor2Sig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘decompTumor2Sig’ ... ** this is package ‘decompTumor2Sig’ version ‘2.25.1’ ** 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 | 2.722 | 0.195 | 4.355 | |
composeGenomesFromExposures | 0.271 | 0.021 | 1.235 | |
computeExplainedVariance | 0.197 | 0.009 | 0.846 | |
convertAlexandrov2Shiraishi | 0.069 | 0.004 | 0.713 | |
convertGenomesFromVRanges | 7.300 | 0.623 | 8.069 | |
decomposeTumorGenomes | 3.376 | 0.369 | 4.441 | |
determineSignatureDistances | 0.076 | 0.005 | 1.134 | |
downgradeShiraishiSignatures | 0.006 | 0.004 | 0.011 | |
evaluateDecompositionQuality | 0.216 | 0.008 | 0.861 | |
getGenomesFromMutFeatData | 0.424 | 0.007 | 0.431 | |
getSignaturesFromEstParam | 0.155 | 0.004 | 0.160 | |
isAlexandrovSet | 0.054 | 0.004 | 0.690 | |
isExposureSet | 3.582 | 0.376 | 4.664 | |
isShiraishiSet | 0.087 | 0.005 | 0.727 | |
isSignatureSet | 0.053 | 0.003 | 0.694 | |
mapSignatureSets | 0.152 | 0.007 | 0.791 | |
plotDecomposedContribution | 0.707 | 0.044 | 1.399 | |
plotExplainedVariance | 78.408 | 0.467 | 79.409 | |
plotMutationDistribution | 3.526 | 0.039 | 4.563 | |
readAlexandrovSignatures | 0.053 | 0.003 | 0.693 | |
readGenomesFromMPF | 2.922 | 0.374 | 3.773 | |
readGenomesFromVCF | 5.42 | 0.53 | 6.47 | |
readShiraishiSignatures | 0.005 | 0.001 | 0.006 | |
sameSignatureFormat | 0.083 | 0.004 | 0.980 | |