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This page was generated on 2025-09-18 12:03 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4808
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4554
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 528/2330HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.25.1  (landing page)
Rosario M. Piro
Snapshot Date: 2025-09-17 13:45 -0400 (Wed, 17 Sep 2025)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: devel
git_last_commit: 3e9ef90
git_last_commit_date: 2025-07-22 22:46:58 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    TIMEOUT  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for decompTumor2Sig on nebbiolo2

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.

raw results


Summary

Package: decompTumor2Sig
Version: 2.25.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decompTumor2Sig_2.25.1.tar.gz
StartedAt: 2025-09-17 23:06:44 -0400 (Wed, 17 Sep 2025)
EndedAt: 2025-09-17 23:21:14 -0400 (Wed, 17 Sep 2025)
EllapsedTime: 870.2 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-3.22-bioc/R/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decompTumor2Sig_2.25.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.25.1’
* 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        93.187  2.334 117.600
convertGenomesFromVRanges     6.798  0.694  12.628
decomposeTumorGenomes         5.155  0.710   7.860
plotMutationDistribution      3.794  0.256   5.619
adjustSignaturesForRegionSet  3.565  0.479   5.038
isExposureSet                 3.448  0.494   5.302
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* 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-3.22-bioc/R/bin/R CMD INSTALL decompTumor2Sig
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘decompTumor2Sig’ ...
** this is package ‘decompTumor2Sig’ version ‘2.25.1’
** 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
adjustSignaturesForRegionSet3.5650.4795.038
composeGenomesFromExposures0.3910.0851.430
computeExplainedVariance0.2850.0120.939
convertAlexandrov2Shiraishi0.1340.0090.884
convertGenomesFromVRanges 6.798 0.69412.628
decomposeTumorGenomes5.1550.7107.860
determineSignatureDistances0.1960.0331.138
downgradeShiraishiSignatures0.0070.0020.010
evaluateDecompositionQuality0.3320.0411.007
getGenomesFromMutFeatData0.3740.0590.434
getSignaturesFromEstParam0.2300.0040.242
isAlexandrovSet0.1110.0220.773
isExposureSet3.4480.4945.302
isShiraishiSet0.1600.0280.864
isSignatureSet0.1190.0260.910
mapSignatureSets0.1980.0230.994
plotDecomposedContribution0.7470.0661.516
plotExplainedVariance 93.187 2.334117.600
plotMutationDistribution3.7940.2565.619
readAlexandrovSignatures0.0920.0210.988
readGenomesFromMPF2.9140.4573.576
readGenomesFromVCF3.3020.4174.071
readShiraishiSignatures0.0050.0000.005
sameSignatureFormat0.1400.0110.847