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This page was generated on 2025-10-17 12:04 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 532/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.25.1  (landing page)
Rosario M. Piro
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 Oct 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 12.7.6 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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decompTumor2Sig_2.25.1.tar.gz
StartedAt: 2025-10-16 22:22:50 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 22:32:55 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 604.6 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decompTumor2Sig_2.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.25.1’
* 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 ... NOTE
File
  inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
* 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 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        71.834  1.792  78.387
convertGenomesFromVRanges     8.020  2.375  23.144
adjustSignaturesForRegionSet  5.947  1.586  17.425
readGenomesFromVCF            5.258  1.826  13.009
readGenomesFromMPF            4.641  2.000  14.358
isExposureSet                 3.661  1.905  12.664
decomposeTumorGenomes         3.089  1.879  17.257
plotMutationDistribution      3.780  0.135   5.300
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/decompTumor2Sig.Rcheck/00check.log’
for details.


Installation output

decompTumor2Sig.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decompTumor2Sig
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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
adjustSignaturesForRegionSet 5.947 1.58617.425
composeGenomesFromExposures0.2310.0361.968
computeExplainedVariance0.2430.0411.418
convertAlexandrov2Shiraishi0.0590.0040.974
convertGenomesFromVRanges 8.020 2.37523.144
decomposeTumorGenomes 3.089 1.87917.257
determineSignatureDistances0.0750.0050.716
downgradeShiraishiSignatures0.0070.0030.010
evaluateDecompositionQuality0.2140.0140.875
getGenomesFromMutFeatData0.4960.1030.620
getSignaturesFromEstParam0.1540.0040.162
isAlexandrovSet0.0560.0060.696
isExposureSet 3.661 1.90512.664
isShiraishiSet0.0840.0050.725
isSignatureSet0.0530.0061.156
mapSignatureSets0.1330.0050.769
plotDecomposedContribution0.8030.0461.762
plotExplainedVariance71.834 1.79278.387
plotMutationDistribution3.7800.1355.300
readAlexandrovSignatures0.0470.0040.932
readGenomesFromMPF 4.641 2.00014.358
readGenomesFromVCF 5.258 1.82613.009
readShiraishiSignatures0.0070.0030.054
sameSignatureFormat0.0910.0071.356