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This page was generated on 2025-10-06 11:41 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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: 2025-10-02 13:40 -0400 (Thu, 02 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-10-03 08:17:28 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 08:26:59 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 571.3 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        105.999  1.155 107.414
convertGenomesFromVRanges      8.980  0.682   9.788
isExposureSet                  4.208  1.246   6.511
decomposeTumorGenomes          4.173  0.272   5.471
adjustSignaturesForRegionSet   3.352  0.603  10.097
plotMutationDistribution       2.824  0.040   5.351
composeGenomesFromExposures    0.261  0.067   7.041
determineSignatureDistances    0.093  0.043   5.910
* 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
###
##############################################################################
##############################################################################


* 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
adjustSignaturesForRegionSet 3.352 0.60310.097
composeGenomesFromExposures0.2610.0677.041
computeExplainedVariance0.2620.0162.045
convertAlexandrov2Shiraishi0.0860.0231.146
convertGenomesFromVRanges8.9800.6829.788
decomposeTumorGenomes4.1730.2725.471
determineSignatureDistances0.0930.0435.910
downgradeShiraishiSignatures0.0130.0000.014
evaluateDecompositionQuality0.3180.0252.389
getGenomesFromMutFeatData0.5860.0200.609
getSignaturesFromEstParam0.1340.0000.137
isAlexandrovSet0.0570.0121.115
isExposureSet4.2081.2466.511
isShiraishiSet0.0930.0162.175
isSignatureSet0.0540.0082.307
mapSignatureSets0.1790.0051.234
plotDecomposedContribution0.6380.1843.789
plotExplainedVariance105.999 1.155107.414
plotMutationDistribution2.8240.0405.351
readAlexandrovSignatures0.0530.0161.835
readGenomesFromMPF3.2600.4033.674
readGenomesFromVCF3.9240.3354.270
readShiraishiSignatures0.0060.0000.006
sameSignatureFormat0.0940.0044.582