Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:21 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE decompTumor2Sig PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 435/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
decompTumor2Sig 2.4.1 Rosario M. Piro
| malbec2 | Linux (Ubuntu 18.04.4 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: 2.4.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_2.4.1.tar.gz |
StartedAt: 2020-10-17 00:20:14 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 00:30:02 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 588.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: decompTumor2Sig.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_2.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/decompTumor2Sig.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (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 ‘2.4.1’ * 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 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 131.416 0.324 131.877 convertGenomesFromVRanges 11.287 0.606 11.904 isExposureSet 6.798 0.353 7.740 decomposeTumorGenomes 6.490 0.389 7.594 readGenomesFromVCF 5.220 0.264 5.487 readGenomesFromMPF 4.682 0.324 5.009 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.11-bioc/meat/decompTumor2Sig.Rcheck/00check.log’ for details.
decompTumor2Sig.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL decompTumor2Sig ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 | |
composeGenomesFromExposures | 0.367 | 0.035 | 1.146 | |
computeExplainedVariance | 0.297 | 0.030 | 0.972 | |
convertAlexandrov2Shiraishi | 0.071 | 0.003 | 0.685 | |
convertGenomesFromVRanges | 11.287 | 0.606 | 11.904 | |
decomposeTumorGenomes | 6.490 | 0.389 | 7.594 | |
determineSignatureDistances | 0.117 | 0.003 | 0.704 | |
downgradeShiraishiSignatures | 0.009 | 0.003 | 0.012 | |
evaluateDecompositionQuality | 0.336 | 0.022 | 0.938 | |
getGenomesFromMutFeatData | 0.925 | 0.009 | 0.936 | |
getSignaturesFromEstParam | 0.261 | 0.002 | 0.263 | |
isAlexandrovSet | 0.057 | 0.003 | 0.706 | |
isExposureSet | 6.798 | 0.353 | 7.740 | |
isShiraishiSet | 0.101 | 0.003 | 0.793 | |
isSignatureSet | 0.054 | 0.002 | 0.770 | |
mapSignatureSets | 0.206 | 0.003 | 0.888 | |
plotDecomposedContribution | 0.515 | 0.012 | 1.227 | |
plotExplainedVariance | 131.416 | 0.324 | 131.877 | |
plotMutationDistribution | 2.287 | 0.011 | 2.926 | |
readAlexandrovSignatures | 0.048 | 0.002 | 0.632 | |
readGenomesFromMPF | 4.682 | 0.324 | 5.009 | |
readGenomesFromVCF | 5.220 | 0.264 | 5.487 | |
readShiraishiSignatures | 0.008 | 0.001 | 0.009 | |
sameSignatureFormat | 0.108 | 0.002 | 0.693 | |