Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-20 15:04:47 -0400 (Mon, 20 Sep 2021).

CHECK results for decompTumor2Sig on nebbiolo1

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.

raw results

Package 457/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.8.0  (landing page)
Rosario M. Piro
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_13
git_last_commit: 974c2b7
git_last_commit_date: 2021-05-19 12:39:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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: 2021-09-19 09:28:22 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 09:34:01 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 339.0 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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     60.905  0.240  62.472
convertGenomesFromVRanges  6.613  0.807   7.422
isExposureSet              4.338  1.866   7.221
readGenomesFromVCF         4.252  0.623   5.273
* 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

##############################################################################
##############################################################################
###
### 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)

Tests output


Example timings

decompTumor2Sig.Rcheck/decompTumor2Sig-Ex.timings

nameusersystemelapsed
adjustSignaturesForRegionSet2.4030.2633.982
composeGenomesFromExposures0.2180.0040.948
computeExplainedVariance0.1610.0080.895
convertAlexandrov2Shiraishi0.0580.0041.087
convertGenomesFromVRanges6.6130.8077.422
decomposeTumorGenomes2.9370.6884.358
determineSignatureDistances0.0820.0010.897
downgradeShiraishiSignatures0.0090.0000.008
evaluateDecompositionQuality0.1900.0000.915
getGenomesFromMutFeatData0.4130.0040.418
getSignaturesFromEstParam0.1450.0000.147
isAlexandrovSet0.0450.0040.772
isExposureSet4.3381.8667.221
isShiraishiSet0.0690.0130.796
isSignatureSet0.0500.0040.780
mapSignatureSets0.1760.0000.901
plotDecomposedContribution0.3470.0161.069
plotExplainedVariance60.905 0.24062.472
plotMutationDistribution1.3150.0122.053
readAlexandrovSignatures0.0440.0080.775
readGenomesFromMPF2.5300.8363.368
readGenomesFromVCF4.2520.6235.273
readShiraishiSignatures0.0080.0000.009
sameSignatureFormat0.1110.0000.867