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CHECK report for decompTumor2Sig on malbec1

This page was generated on 2021-05-06 12:27:19 -0400 (Thu, 06 May 2021).

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 439/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.6.0  (landing page)
Rosario M. Piro
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/decompTumor2Sig
Branch: RELEASE_3_12
Last Commit: f498786
Last Changed Date: 2020-10-27 11:40:56 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: decompTumor2Sig
Version: 2.6.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings decompTumor2Sig_2.6.0.tar.gz
StartedAt: 2021-05-06 00:44:11 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:51:56 -0400 (Thu, 06 May 2021)
EllapsedTime: 465.5 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings decompTumor2Sig_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.6.0’
* 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     97.404  0.004  97.581
convertGenomesFromVRanges  9.224  0.248   9.501
* 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


Installation output

decompTumor2Sig.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL decompTumor2Sig
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* installing to library ‘/home/biocbuild/bbs-3.12-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)

Tests output


Example timings

decompTumor2Sig.Rcheck/decompTumor2Sig-Ex.timings

nameusersystemelapsed
composeGenomesFromExposures0.4200.0041.224
computeExplainedVariance1.3200.0082.137
convertAlexandrov2Shiraishi0.1560.0000.938
convertGenomesFromVRanges9.2240.2489.501
decomposeTumorGenomes3.9640.1844.858
determineSignatureDistances0.1600.0040.792
downgradeShiraishiSignatures0.0120.0000.023
evaluateDecompositionQuality0.3520.0081.157
getGenomesFromMutFeatData0.7960.0000.811
getSignaturesFromEstParam0.2560.0040.269
isAlexandrovSet0.1120.0080.906
isExposureSet3.8120.1244.673
isShiraishiSet0.1600.0040.848
isSignatureSet0.1160.0080.806
mapSignatureSets0.2040.0080.898
plotDecomposedContribution0.5560.0201.363
plotExplainedVariance97.404 0.00497.581
plotMutationDistribution2.0520.0042.800
readAlexandrovSignatures0.1120.0080.807
readGenomesFromMPF3.4480.1443.604
readGenomesFromVCF4.5480.1684.721
readShiraishiSignatures0.0040.0000.006
sameSignatureFormat0.1320.0000.926