Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-06 17:38 -0400 (Tue, 06 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4756 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4490 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4519 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4468 |
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 522/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decompTumor2Sig 2.20.0 (landing page) Rosario M. Piro
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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: 2.20.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings decompTumor2Sig_2.20.0.tar.gz |
StartedAt: 2024-08-04 22:50:19 -0400 (Sun, 04 Aug 2024) |
EndedAt: 2024-08-04 23:00:35 -0400 (Sun, 04 Aug 2024) |
EllapsedTime: 615.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings decompTumor2Sig_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/decompTumor2Sig.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 ‘decompTumor2Sig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decompTumor2Sig’ version ‘2.20.0’ * 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 ‘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 ... OK * 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 loading without being on the library search path ... 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 61.556 0.975 62.534 convertGenomesFromVRanges 6.452 1.124 7.578 * 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: OK
decompTumor2Sig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 2.564 | 0.260 | 4.241 | |
composeGenomesFromExposures | 0.281 | 0.020 | 1.198 | |
computeExplainedVariance | 0.235 | 0.000 | 0.951 | |
convertAlexandrov2Shiraishi | 0.112 | 0.012 | 0.836 | |
convertGenomesFromVRanges | 6.452 | 1.124 | 7.578 | |
decomposeTumorGenomes | 2.751 | 0.676 | 4.140 | |
determineSignatureDistances | 0.131 | 0.028 | 0.938 | |
downgradeShiraishiSignatures | 0.005 | 0.004 | 0.009 | |
evaluateDecompositionQuality | 0.270 | 0.025 | 1.009 | |
getGenomesFromMutFeatData | 0.382 | 0.047 | 0.431 | |
getSignaturesFromEstParam | 0.127 | 0.004 | 0.132 | |
isAlexandrovSet | 0.088 | 0.012 | 0.823 | |
isExposureSet | 2.730 | 0.536 | 3.986 | |
isShiraishiSet | 0.110 | 0.016 | 0.840 | |
isSignatureSet | 0.090 | 0.002 | 0.814 | |
mapSignatureSets | 0.183 | 0.015 | 1.033 | |
plotDecomposedContribution | 0.399 | 0.024 | 1.137 | |
plotExplainedVariance | 61.556 | 0.975 | 62.534 | |
plotMutationDistribution | 1.789 | 0.020 | 2.590 | |
readAlexandrovSignatures | 0.087 | 0.001 | 0.809 | |
readGenomesFromMPF | 2.454 | 0.636 | 3.091 | |
readGenomesFromVCF | 3.027 | 0.632 | 3.658 | |
readShiraishiSignatures | 0.005 | 0.000 | 0.005 | |
sameSignatureFormat | 0.149 | 0.024 | 0.880 | |