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This page was generated on 2021-09-20 15:05:39 -0400 (Mon, 20 Sep 2021).

CHECK results for decompTumor2Sig on machv2

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? here 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 457/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.8.0  (landing page)
Rosario M. Piro
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_13
git_last_commit: 974c2b7
git_last_commit_date: 2021-05-19 12:39:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decompTumor2Sig
Version: 2.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz
StartedAt: 2021-09-19 18:04:49 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 18:13:08 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 499.9 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:decompTumor2Sig.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings decompTumor2Sig_2.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decompTumor2Sig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decompTumor2Sig’ version ‘2.8.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 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     110.585  0.258 110.914
convertGenomesFromVRanges   9.363  0.537   9.906
decomposeTumorGenomes       5.888  0.313   7.536
isExposureSet               4.791  0.259   5.893
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/decompTumor2Sig.Rcheck/00check.log’
for details.



Installation output

decompTumor2Sig.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
adjustSignaturesForRegionSet2.4800.2203.524
composeGenomesFromExposures0.3730.0211.155
computeExplainedVariance0.3160.0111.040
convertAlexandrov2Shiraishi0.0880.0040.796
convertGenomesFromVRanges9.3630.5379.906
decomposeTumorGenomes5.8880.3137.536
determineSignatureDistances0.0860.0040.802
downgradeShiraishiSignatures0.0100.0040.014
evaluateDecompositionQuality0.2750.0101.007
getGenomesFromMutFeatData0.7880.0110.800
getSignaturesFromEstParam0.1950.0020.198
isAlexandrovSet0.0560.0030.762
isExposureSet4.7910.2595.893
isShiraishiSet0.0950.0031.282
isSignatureSet0.0490.0030.894
mapSignatureSets0.2110.0041.390
plotDecomposedContribution0.5040.0131.230
plotExplainedVariance110.585 0.258110.914
plotMutationDistribution2.0430.0232.862
readAlexandrovSignatures0.0410.0021.122
readGenomesFromMPF4.0640.2514.325
readGenomesFromVCF4.5030.2594.764
readShiraishiSignatures0.0070.0010.008
sameSignatureFormat0.0880.0030.796