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This page was generated on 2022-05-18 12:06:35 -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 palomino3


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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.12.0.tar.gz
StartedAt: 2022-05-17 23:12:14 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 23:18:41 -0400 (Tue, 17 May 2022)
EllapsedTime: 386.6 seconds
RetCode: 0
Status:   OK  
CheckDir: decompTumor2Sig.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decompTumor2Sig.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings decompTumor2Sig_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/decompTumor2Sig.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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     69.35   0.91   70.27
convertGenomesFromVRanges  6.84   0.64    7.52
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/decompTumor2Sig.Rcheck/00check.log'
for details.



Installation output

decompTumor2Sig.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL decompTumor2Sig
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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
adjustSignaturesForRegionSet3.060.334.22
composeGenomesFromExposures0.300.020.80
computeExplainedVariance0.160.010.64
convertAlexandrov2Shiraishi0.060.020.55
convertGenomesFromVRanges6.840.647.52
decomposeTumorGenomes3.310.394.25
determineSignatureDistances0.080.000.64
downgradeShiraishiSignatures0.020.000.02
evaluateDecompositionQuality0.230.000.72
getGenomesFromMutFeatData0.420.010.51
getSignaturesFromEstParam0.130.000.24
isAlexandrovSet0.040.000.60
isExposureSet3.710.494.74
isShiraishiSet0.090.001.66
isSignatureSet0.050.000.53
mapSignatureSets0.150.010.72
plotDecomposedContribution0.330.020.89
plotExplainedVariance69.35 0.9170.27
plotMutationDistribution1.540.012.01
readAlexandrovSignatures0.030.000.52
readGenomesFromMPF2.430.332.76
readGenomesFromVCF4.120.334.46
readShiraishiSignatures0.000.010.01
sameSignatureFormat0.130.031.64