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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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

Package 528/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.24.0  (landing page)
Rosario M. Piro
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_21
git_last_commit: c68d8e2
git_last_commit_date: 2025-04-15 11:39:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    TIMEOUT  skippedskipped
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for decompTumor2Sig on kunpeng2

To the developers/maintainers of the decompTumor2Sig package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: decompTumor2Sig
Version: 2.24.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decompTumor2Sig_2.24.0.tar.gz
StartedAt: 2025-10-14 08:15:42 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 08:25:21 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 579.3 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings decompTumor2Sig_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/decompTumor2Sig.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.24.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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        108.934  2.039 111.214
convertGenomesFromVRanges      7.662  0.856   8.690
isExposureSet                  5.360  0.702   7.137
decomposeTumorGenomes          5.559  0.391   7.994
plotMutationDistribution       4.633  0.028   6.574
adjustSignaturesForRegionSet   3.035  0.344   7.545
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL decompTumor2Sig
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘decompTumor2Sig’ ...
** this is package ‘decompTumor2Sig’ version ‘2.24.0’
** 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
adjustSignaturesForRegionSet3.0350.3447.545
composeGenomesFromExposures0.3240.0163.354
computeExplainedVariance0.2800.0121.344
convertAlexandrov2Shiraishi0.0730.0162.796
convertGenomesFromVRanges7.6620.8568.690
decomposeTumorGenomes5.5590.3917.994
determineSignatureDistances0.1060.0031.191
downgradeShiraishiSignatures0.010.000.01
evaluateDecompositionQuality0.2470.0253.009
getGenomesFromMutFeatData0.6220.0110.639
getSignaturesFromEstParam0.1260.0000.128
isAlexandrovSet0.0550.0043.177
isExposureSet5.3600.7027.137
isShiraishiSet0.0840.0601.185
isSignatureSet0.0560.0041.093
mapSignatureSets0.1890.0121.225
plotDecomposedContribution0.8600.1072.337
plotExplainedVariance108.934 2.039111.214
plotMutationDistribution4.6330.0286.574
readAlexandrovSignatures0.0510.0042.115
readGenomesFromMPF3.1320.1963.336
readGenomesFromVCF4.0610.2154.288
readShiraishiSignatures0.0050.0000.006
sameSignatureFormat0.0920.0002.156