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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the decompTumor2Sig package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 457/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
decompTumor2Sig 2.8.0 (landing page) Rosario M. Piro
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: decompTumor2Sig |
Version: 2.8.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz |
StartedAt: 2021-10-14 09:30:03 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:35:42 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 339.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/decompTumor2Sig.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decompTumor2Sig’ version ‘2.8.0’ * 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotExplainedVariance 61.218 0.080 62.004 convertGenomesFromVRanges 6.900 0.867 7.768 isExposureSet 3.941 0.676 5.423 * 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: OK
decompTumor2Sig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-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 | 2.763 | 1.003 | 4.962 | |
composeGenomesFromExposures | 0.248 | 0.012 | 1.280 | |
computeExplainedVariance | 0.163 | 0.000 | 0.892 | |
convertAlexandrov2Shiraishi | 0.059 | 0.001 | 0.786 | |
convertGenomesFromVRanges | 6.900 | 0.867 | 7.768 | |
decomposeTumorGenomes | 2.982 | 0.620 | 4.330 | |
determineSignatureDistances | 0.076 | 0.003 | 0.886 | |
downgradeShiraishiSignatures | 0.011 | 0.004 | 0.016 | |
evaluateDecompositionQuality | 0.204 | 0.007 | 0.935 | |
getGenomesFromMutFeatData | 0.394 | 0.007 | 0.403 | |
getSignaturesFromEstParam | 0.135 | 0.000 | 0.137 | |
isAlexandrovSet | 0.042 | 0.004 | 0.782 | |
isExposureSet | 3.941 | 0.676 | 5.423 | |
isShiraishiSet | 0.089 | 0.000 | 0.834 | |
isSignatureSet | 0.047 | 0.004 | 0.968 | |
mapSignatureSets | 0.136 | 0.005 | 0.867 | |
plotDecomposedContribution | 0.338 | 0.000 | 1.063 | |
plotExplainedVariance | 61.218 | 0.080 | 62.004 | |
plotMutationDistribution | 2.470 | 0.000 | 4.358 | |
readAlexandrovSignatures | 0.064 | 0.000 | 0.785 | |
readGenomesFromMPF | 3.221 | 0.884 | 4.219 | |
readGenomesFromVCF | 3.065 | 0.611 | 3.680 | |
readShiraishiSignatures | 0.001 | 0.004 | 0.005 | |
sameSignatureFormat | 0.085 | 0.001 | 0.794 | |