Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 2.22.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings decompTumor2Sig_2.22.0.tar.gz |
StartedAt: 2024-11-20 01:30:38 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:40:31 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 592.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings decompTumor2Sig_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/decompTumor2Sig.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 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 51.578 0.721 55.073 convertGenomesFromVRanges 5.290 0.378 6.973 * 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-3.20-bioc/R/bin/R CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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 | 1.929 | 0.170 | 4.776 | |
composeGenomesFromExposures | 0.181 | 0.014 | 0.857 | |
computeExplainedVariance | 0.150 | 0.003 | 1.108 | |
convertAlexandrov2Shiraishi | 0.075 | 0.004 | 0.625 | |
convertGenomesFromVRanges | 5.290 | 0.378 | 6.973 | |
decomposeTumorGenomes | 1.899 | 0.172 | 3.242 | |
determineSignatureDistances | 0.085 | 0.001 | 0.967 | |
downgradeShiraishiSignatures | 0.003 | 0.002 | 0.009 | |
evaluateDecompositionQuality | 0.157 | 0.003 | 1.113 | |
getGenomesFromMutFeatData | 0.285 | 0.001 | 0.368 | |
getSignaturesFromEstParam | 0.072 | 0.000 | 0.076 | |
isAlexandrovSet | 0.066 | 0.001 | 0.606 | |
isExposureSet | 1.810 | 0.164 | 3.049 | |
isShiraishiSet | 0.096 | 0.002 | 0.659 | |
isSignatureSet | 0.362 | 0.022 | 1.172 | |
mapSignatureSets | 0.117 | 0.002 | 1.039 | |
plotDecomposedContribution | 0.298 | 0.000 | 1.159 | |
plotExplainedVariance | 51.578 | 0.721 | 55.073 | |
plotMutationDistribution | 1.358 | 0.007 | 2.513 | |
readAlexandrovSignatures | 0.106 | 0.002 | 0.796 | |
readGenomesFromMPF | 1.510 | 0.142 | 1.729 | |
readGenomesFromVCF | 1.885 | 0.170 | 2.281 | |
readShiraishiSignatures | 0.002 | 0.001 | 0.004 | |
sameSignatureFormat | 0.085 | 0.001 | 0.928 | |