Back to Multiple platform build/check report for BioC 3.15
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-05-18 12:08:02 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for decompTumor2Sig on merida1


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? 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 483/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
decompTumor2Sig 2.12.0  (landing page)
Rosario M. Piro
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/decompTumor2Sig
git_branch: RELEASE_3_15
git_last_commit: 8b41d1c
git_last_commit_date: 2022-04-26 11:52:21 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: decompTumor2Sig
Version: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2022-05-18 01:13:06 -0400 (Wed, 18 May 2022)
EndedAt: 2022-05-18 01:24:54 -0400 (Wed, 18 May 2022)
EllapsedTime: 707.7 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/decompTumor2Sig.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.12.0’
* 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 ... 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        168.582  0.446 170.903
convertGenomesFromVRanges     10.873  1.334  13.615
isExposureSet                  6.884  1.087   9.996
decomposeTumorGenomes          6.255  0.966   9.368
readGenomesFromMPF             5.550  1.604  10.761
readGenomesFromVCF             6.278  0.367   6.974
adjustSignaturesForRegionSet   2.745  0.273   9.765
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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
adjustSignaturesForRegionSet2.7450.2739.765
composeGenomesFromExposures0.4430.0171.198
computeExplainedVariance0.3630.0111.075
convertAlexandrov2Shiraishi0.1060.0050.788
convertGenomesFromVRanges10.873 1.33413.615
decomposeTumorGenomes6.2550.9669.368
determineSignatureDistances0.1210.0030.799
downgradeShiraishiSignatures0.0120.0020.014
evaluateDecompositionQuality0.3590.0060.989
getGenomesFromMutFeatData1.0570.0151.074
getSignaturesFromEstParam0.2930.0030.295
isAlexandrovSet0.0640.0030.831
isExposureSet6.8841.0879.996
isShiraishiSet0.1150.0040.788
isSignatureSet0.0620.0030.690
mapSignatureSets0.2460.0030.935
plotDecomposedContribution0.6810.0211.335
plotExplainedVariance168.582 0.446170.903
plotMutationDistribution3.0930.0213.870
readAlexandrovSignatures0.0630.0030.729
readGenomesFromMPF 5.550 1.60410.761
readGenomesFromVCF6.2780.3676.974
readShiraishiSignatures0.0070.0000.008
sameSignatureFormat0.1190.0020.748