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This page was generated on 2023-02-06 11:05:05 -0500 (Mon, 06 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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

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? 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 481/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.15.0  (landing page)
Rosario M. Piro
Snapshot Date: 2023-02-05 14:00:11 -0500 (Sun, 05 Feb 2023)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: master
git_last_commit: f413c6a
git_last_commit_date: 2022-11-01 11:18:56 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decompTumor2Sig
Version: 2.15.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings decompTumor2Sig_2.15.0.tar.gz
StartedAt: 2023-02-05 20:04:02 -0500 (Sun, 05 Feb 2023)
EndedAt: 2023-02-05 20:13:55 -0500 (Sun, 05 Feb 2023)
EllapsedTime: 592.9 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings decompTumor2Sig_2.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decompTumor2Sig.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.15.0’
* 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     67.396  1.453  68.853
convertGenomesFromVRanges  6.284  1.183   7.476
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decompTumor2Sig.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

decompTumor2Sig.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL decompTumor2Sig
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
adjustSignaturesForRegionSet2.4990.4244.548
composeGenomesFromExposures0.2510.0401.180
computeExplainedVariance0.2490.0401.344
convertAlexandrov2Shiraishi0.1140.0211.022
convertGenomesFromVRanges6.2841.1837.476
decomposeTumorGenomes3.1490.6854.720
determineSignatureDistances0.1470.0281.053
downgradeShiraishiSignatures0.0010.0110.011
evaluateDecompositionQuality0.2850.0761.233
getGenomesFromMutFeatData0.4410.1320.574
getSignaturesFromEstParam0.1210.0000.122
isAlexandrovSet0.1370.0001.032
isExposureSet2.9321.0254.718
isShiraishiSet0.1790.0091.059
isSignatureSet0.1160.0081.009
mapSignatureSets0.2480.0291.034
plotDecomposedContribution0.5410.1471.748
plotExplainedVariance67.396 1.45368.853
plotMutationDistribution2.2390.0643.271
readAlexandrovSignatures0.1330.0171.029
readGenomesFromMPF2.2880.8003.123
readGenomesFromVCF2.7920.5243.316
readShiraishiSignatures0.0040.0000.005
sameSignatureFormat0.1580.0281.073